Starting phenix.real_space_refine
on Thu Mar 13 07:44:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pqy_20456/03_2025/6pqy_20456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pqy_20456/03_2025/6pqy_20456.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pqy_20456/03_2025/6pqy_20456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pqy_20456/03_2025/6pqy_20456.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pqy_20456/03_2025/6pqy_20456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pqy_20456/03_2025/6pqy_20456.cif"
  }
  resolution = 4.2
  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=   0.002
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      64      5.49       5
     S      34      5.16       5
     C    5324      2.51       5
     N    1496      2.21       5
     O    1772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8690
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 3689
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 442}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 333
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "C"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 323
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "D"
      Number of atoms: 3689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 3689
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 442}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 333
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
    Chain: "F"
      Number of atoms: 323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 323
          Classifications: {'DNA': 16}
          Link IDs: {'rna3p': 15}
  Time building chain proxies: 5.66, per 1000 atoms: 0.65
  Number of scatterers: 8690
  At special positions: 0
  Unit cell: (85.05, 122.85, 92.4, 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      64     15.00
     O    1772      8.00
     N    1496      7.00
     C    5324      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: 2.40
  Conformation dependent library (CDL) restraints added in 852.2 milliseconds
  

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1764

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 4 sheets defined
      52.6% alpha, 14.8% beta
      28 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 3.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 37
      removed outlier: 4.031A  pdb=" N   GLY A  31 " --> pdb=" O   GLU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 53
      removed outlier: 3.582A  pdb=" N   GLU A  53 " --> pdb=" O   THR A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 73
      removed outlier: 3.722A  pdb=" N   VAL A  65 " --> pdb=" O   SER A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 106
      removed outlier: 4.271A  pdb=" N   ILE A 105 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 175
      removed outlier: 4.030A  pdb=" N   TYR A 174 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 201
    Processing helix  chain 'A' and resid 226 through 232
    Processing helix  chain 'A' and resid 272 through 274
      No H-bonds generated for 'chain 'A' and resid 272 through 274'
    Processing helix  chain 'A' and resid 275 through 289
      removed outlier: 3.697A  pdb=" N   VAL A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 322
      removed outlier: 3.690A  pdb=" N   ASN A 322 " --> pdb=" O   LYS A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 344
    Processing helix  chain 'A' and resid 347 through 355
    Processing helix  chain 'A' and resid 358 through 374
      removed outlier: 3.504A  pdb=" N   ILE A 362 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   THR A 373 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER A 374 " --> pdb=" O   GLN A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 398
    Processing helix  chain 'A' and resid 404 through 412
      removed outlier: 3.571A  pdb=" N   HIS A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 421
      removed outlier: 3.512A  pdb=" N   GLU A 420 " --> pdb=" O   ASP A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 448
    Processing helix  chain 'A' and resid 454 through 470
      removed outlier: 3.892A  pdb=" N   ASN A 458 " --> pdb=" O   ARG A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 496
      removed outlier: 3.554A  pdb=" N   LEU A 495 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 25 through 37
      removed outlier: 4.031A  pdb=" N   GLY D  31 " --> pdb=" O   GLU D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 39 through 53
      removed outlier: 3.582A  pdb=" N   GLU D  53 " --> pdb=" O   THR D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 73
      removed outlier: 3.721A  pdb=" N   VAL D  65 " --> pdb=" O   SER D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 106
      removed outlier: 4.270A  pdb=" N   ILE D 105 " --> pdb=" O   ILE D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 175
      removed outlier: 4.031A  pdb=" N   TYR D 174 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 186 through 201
    Processing helix  chain 'D' and resid 226 through 232
    Processing helix  chain 'D' and resid 272 through 274
      No H-bonds generated for 'chain 'D' and resid 272 through 274'
    Processing helix  chain 'D' and resid 275 through 289
      removed outlier: 3.698A  pdb=" N   VAL D 279 " --> pdb=" O   ALA D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 302 through 322
      removed outlier: 3.690A  pdb=" N   ASN D 322 " --> pdb=" O   LYS D 318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 344
    Processing helix  chain 'D' and resid 347 through 355
    Processing helix  chain 'D' and resid 358 through 374
      removed outlier: 3.505A  pdb=" N   ILE D 362 " --> pdb=" O   ASP D 358 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE D 372 " --> pdb=" O   ILE D 368 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   THR D 373 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER D 374 " --> pdb=" O   GLN D 370 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 379 through 398
    Processing helix  chain 'D' and resid 404 through 412
      removed outlier: 3.572A  pdb=" N   HIS D 408 " --> pdb=" O   SER D 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 413 through 421
      removed outlier: 3.512A  pdb=" N   GLU D 420 " --> pdb=" O   ASP D 416 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 430 through 448
    Processing helix  chain 'D' and resid 454 through 470
      removed outlier: 3.892A  pdb=" N   ASN D 458 " --> pdb=" O   ARG D 454 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 489 through 496
      removed outlier: 3.554A  pdb=" N   LEU D 495 " --> pdb=" O   GLU D 491 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81
      removed outlier: 6.408A  pdb=" N   THR A 149 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE A 180 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   PHE A 147 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81
      removed outlier: 6.408A  pdb=" N   THR A 149 " --> pdb=" O   VAL A 178 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE A 180 " --> pdb=" O   PHE A 147 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   PHE A 147 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASP A 125 " --> pdb=" O   MET A 148 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ILE A 119 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   LEU A 156 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ILE A 117 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 10.174A  pdb=" N   LEU A 116 " --> pdb=" O   HIS A 216 " (cutoff:3.500A)
      removed outlier: 11.586A  pdb=" N   LEU A 218 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      removed outlier: 10.387A  pdb=" N   LEU A 118 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 11.390A  pdb=" N   MET A 220 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
      removed outlier: 11.195A  pdb=" N   SER A 120 " --> pdb=" O   MET A 220 " (cutoff:3.500A)
      removed outlier: 8.487A  pdb=" N   MET A 222 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   TRP A 122 " --> pdb=" O   MET A 222 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 80 through 81
      removed outlier: 6.408A  pdb=" N   THR D 149 " --> pdb=" O   VAL D 178 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE D 180 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   PHE D 147 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 80 through 81
      removed outlier: 6.408A  pdb=" N   THR D 149 " --> pdb=" O   VAL D 178 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE D 180 " --> pdb=" O   PHE D 147 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   PHE D 147 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASP D 125 " --> pdb=" O   MET D 148 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ILE D 119 " --> pdb=" O   LEU D 154 " (cutoff:3.500A)
      removed outlier: 5.024A  pdb=" N   LEU D 156 " --> pdb=" O   ILE D 117 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ILE D 117 " --> pdb=" O   LEU D 156 " (cutoff:3.500A)
      removed outlier: 10.174A  pdb=" N   LEU D 116 " --> pdb=" O   HIS D 216 " (cutoff:3.500A)
      removed outlier: 11.587A  pdb=" N   LEU D 218 " --> pdb=" O   LEU D 116 " (cutoff:3.500A)
      removed outlier: 10.386A  pdb=" N   LEU D 118 " --> pdb=" O   LEU D 218 " (cutoff:3.500A)
      removed outlier: 11.390A  pdb=" N   MET D 220 " --> pdb=" O   LEU D 118 " (cutoff:3.500A)
      removed outlier: 11.194A  pdb=" N   SER D 120 " --> pdb=" O   MET D 220 " (cutoff:3.500A)
      removed outlier: 8.488A  pdb=" N   MET D 222 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   TRP D 122 " --> pdb=" O   MET D 222 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    1044 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      70 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 2.99

  Time building geometry restraints manager: 2.82 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: 2151
        1.33 -     1.45: 1973
        1.45 -     1.57: 4688
        1.57 -     1.69: 124
        1.69 -     1.81: 52
  Bond restraints: 8988
  Sorted by residual:
  bond pdb=" O3'  DC F  12 "
       pdb=" P    DC F  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.647 -0.040 1.50e-02 4.44e+03 7.16e+00
  bond pdb=" O3'  DC C  12 "
       pdb=" P    DC C  13 "
    ideal  model  delta    sigma   weight residual
    1.607  1.644 -0.037 1.50e-02 4.44e+03 6.15e+00
  bond pdb=" C1'  DT B  22 "
       pdb=" N1   DT B  22 "
    ideal  model  delta    sigma   weight residual
    1.490  1.441  0.049 3.00e-02 1.11e+03 2.67e+00
  bond pdb=" C1'  DT E  22 "
       pdb=" N1   DT E  22 "
    ideal  model  delta    sigma   weight residual
    1.490  1.441  0.049 3.00e-02 1.11e+03 2.63e+00
  bond pdb=" CB  TRP D  41 "
       pdb=" CG  TRP D  41 "
    ideal  model  delta    sigma   weight residual
    1.498  1.449  0.049 3.10e-02 1.04e+03 2.47e+00
  ... (remaining 8983 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 11886
        2.26 -     4.51: 471
        4.51 -     6.77: 30
        6.77 -     9.03: 8
        9.03 -    11.29: 5
  Bond angle restraints: 12400
  Sorted by residual:
  angle pdb=" C4'  DC F  12 "
        pdb=" C3'  DC F  12 "
        pdb=" O3'  DC F  12 "
      ideal   model   delta    sigma   weight residual
     110.00  121.29  -11.29 1.50e+00 4.44e-01 5.66e+01
  angle pdb=" C4'  DC C  12 "
        pdb=" C3'  DC C  12 "
        pdb=" O3'  DC C  12 "
      ideal   model   delta    sigma   weight residual
     110.00  120.69  -10.69 1.50e+00 4.44e-01 5.08e+01
  angle pdb=" O3'  DT C  15 "
        pdb=" C3'  DT C  15 "
        pdb=" C2'  DT C  15 "
      ideal   model   delta    sigma   weight residual
     111.50  120.80   -9.30 1.50e+00 4.44e-01 3.84e+01
  angle pdb=" C3'  DC F  12 "
        pdb=" C2'  DC F  12 "
        pdb=" C1'  DC F  12 "
      ideal   model   delta    sigma   weight residual
     101.60  107.16   -5.56 1.50e+00 4.44e-01 1.37e+01
  angle pdb=" C3'  DC C  12 "
        pdb=" C2'  DC C  12 "
        pdb=" C1'  DC C  12 "
      ideal   model   delta    sigma   weight residual
     101.60  106.93   -5.33 1.50e+00 4.44e-01 1.26e+01
  ... (remaining 12395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 4952
       35.87 -    71.75: 328
       71.75 -   107.62: 10
      107.62 -   143.49: 0
      143.49 -   179.36: 10
  Dihedral angle restraints: 5300
    sinusoidal: 2588
      harmonic: 2712
  Sorted by residual:
  dihedral pdb=" CA  ASP D 161 "
           pdb=" C   ASP D 161 "
           pdb=" N   THR D 162 "
           pdb=" CA  THR D 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.62   25.38     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  ASP A 161 "
           pdb=" C   ASP A 161 "
           pdb=" N   THR A 162 "
           pdb=" CA  THR A 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.62   25.38     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  SER A 453 "
           pdb=" C   SER A 453 "
           pdb=" N   ARG A 454 "
           pdb=" CA  ARG A 454 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.18   24.82     0      5.00e+00 4.00e-02 2.46e+01
  ... (remaining 5297 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1122
       0.073 -    0.146: 238
       0.146 -    0.219: 31
       0.219 -    0.292: 6
       0.292 -    0.364: 3
  Chirality restraints: 1400
  Sorted by residual:
  chirality pdb=" C3'  DC F  12 "
            pdb=" C4'  DC F  12 "
            pdb=" O3'  DC F  12 "
            pdb=" C2'  DC F  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.30   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" C3'  DC C  12 "
            pdb=" C4'  DC C  12 "
            pdb=" O3'  DC C  12 "
            pdb=" C2'  DC C  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.30   -0.36 2.00e-01 2.50e+01 3.32e+00
  chirality pdb=" C3'  DT C  15 "
            pdb=" C4'  DT C  15 "
            pdb=" O3'  DT C  15 "
            pdb=" C2'  DT C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.34   -0.33 2.00e-01 2.50e+01 2.64e+00
  ... (remaining 1397 not shown)

  Planarity restraints: 1348
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC C  12 "    0.041 2.00e-02 2.50e+03   2.75e-02 1.71e+01
        pdb=" N1   DC C  12 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2   DC C  12 "    0.002 2.00e-02 2.50e+03
        pdb=" O2   DC C  12 "   -0.033 2.00e-02 2.50e+03
        pdb=" N3   DC C  12 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DC C  12 "    0.047 2.00e-02 2.50e+03
        pdb=" N4   DC C  12 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DC C  12 "   -0.025 2.00e-02 2.50e+03
        pdb=" C6   DC C  12 "   -0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C  15 "   -0.051 2.00e-02 2.50e+03   2.26e-02 1.28e+01
        pdb=" N1   DT C  15 "    0.024 2.00e-02 2.50e+03
        pdb=" C2   DT C  15 "    0.018 2.00e-02 2.50e+03
        pdb=" O2   DT C  15 "    0.011 2.00e-02 2.50e+03
        pdb=" N3   DT C  15 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4   DT C  15 "    0.000 2.00e-02 2.50e+03
        pdb=" O4   DT C  15 "   -0.026 2.00e-02 2.50e+03
        pdb=" C5   DT C  15 "    0.013 2.00e-02 2.50e+03
        pdb=" C7   DT C  15 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DT C  15 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA B  30 "    0.019 2.00e-02 2.50e+03   2.07e-02 1.18e+01
        pdb=" N9   DA B  30 "   -0.053 2.00e-02 2.50e+03
        pdb=" C8   DA B  30 "    0.037 2.00e-02 2.50e+03
        pdb=" N7   DA B  30 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5   DA B  30 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DA B  30 "    0.001 2.00e-02 2.50e+03
        pdb=" N6   DA B  30 "    0.001 2.00e-02 2.50e+03
        pdb=" N1   DA B  30 "    0.005 2.00e-02 2.50e+03
        pdb=" C2   DA B  30 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DA B  30 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA B  30 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1345 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1501
        2.76 -     3.30: 9795
        3.30 -     3.83: 15952
        3.83 -     4.37: 17791
        4.37 -     4.90: 25995
  Nonbonded interactions: 71034
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 149 "
            pdb=" OE1 GLN A 179 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG1 THR D 149 "
            pdb=" OE1 GLN D 179 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" N   ASP D 500 "
            pdb=" OD1 ASP D 500 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" N   ASP A 500 "
            pdb=" OD1 ASP A 500 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   VAL D  81 "
            pdb=" NE2 GLN D 455 "
     model   vdw
     2.244 3.120
  ... (remaining 71029 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}

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:             1.090
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.700
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
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      :  0.007   0.049   8988  Z= 0.448
  Angle     :  0.987  11.285  12400  Z= 0.578
  Chirality :  0.064   0.364   1400
  Planarity :  0.007   0.066   1348
  Dihedral  : 22.029 179.364   3536
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 25.09
  Ramachandran Plot:
    Outliers :  0.66 %
    Allowed  :  6.83 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  5.38 %
    Favored  : 94.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.46 (0.22), residues: 908
  helix: -2.68 (0.18), residues: 438
  sheet: -3.07 (0.55), residues: 60
  loop : -3.19 (0.26), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP D  41 
 HIS   0.015   0.003   HIS A 448 
 PHE   0.028   0.003   PHE A 102 
 TYR   0.023   0.005   TYR A 174 
 ARG   0.044   0.008   ARG A 343 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 143
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 MET cc_start: 0.8183 (mmm) cc_final: 0.7776 (mmp)
REVERT: A  280 MET cc_start: 0.7800 (ppp) cc_final: 0.7234 (ppp)
REVERT: A  337 ASP cc_start: 0.4447 (m-30) cc_final: 0.3873 (m-30)
REVERT: D  193 GLU cc_start: 0.9064 (tp30) cc_final: 0.8540 (tp30)
REVERT: D  197 MET cc_start: 0.8507 (mmm) cc_final: 0.7847 (mmp)
REVERT: D  204 LEU cc_start: 0.8835 (pp) cc_final: 0.8560 (pt)
REVERT: D  280 MET cc_start: 0.7380 (ppp) cc_final: 0.6939 (ppp)
REVERT: D  337 ASP cc_start: 0.3946 (m-30) cc_final: 0.3736 (m-30)
  outliers start: 4
  outliers final: 1
  residues processed: 147
  average time/residue: 0.2725
  time to fit residues: 53.0991
Evaluate side-chains
  90 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0970
   chunk 24 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    6.9990
   chunk 75 optimal weight:    0.1980
   chunk 29 optimal weight:    0.1980
   chunk 45 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 166 ASN
A 307 HIS
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 166 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.131968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.100906 restraints weight = 29742.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.104561 restraints weight = 15732.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.106890 restraints weight = 10168.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8988  Z= 0.184
  Angle     :  0.646   6.188  12400  Z= 0.356
  Chirality :  0.041   0.147   1400
  Planarity :  0.004   0.055   1348
  Dihedral  : 25.301 179.323   1688
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.39 (0.26), residues: 908
  helix: -0.83 (0.22), residues: 452
  sheet: -2.14 (0.60), residues: 54
  loop : -2.36 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 400 
 HIS   0.006   0.001   HIS D 408 
 PHE   0.013   0.002   PHE A 347 
 TYR   0.012   0.001   TYR A 288 
 ARG   0.006   0.001   ARG A 100 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.8547 (tp) cc_final: 0.8319 (tp)
REVERT: A   32 LEU cc_start: 0.8842 (tp) cc_final: 0.8568 (tt)
REVERT: A  103 GLU cc_start: 0.8742 (pt0) cc_final: 0.8419 (pp20)
REVERT: A  106 ARG cc_start: 0.7593 (mmp-170) cc_final: 0.7046 (tmt170)
REVERT: A  115 GLN cc_start: 0.6720 (tp40) cc_final: 0.6102 (tp-100)
REVERT: A  124 PHE cc_start: 0.8992 (p90) cc_final: 0.8772 (p90)
REVERT: A  176 ARG cc_start: 0.8566 (mtp85) cc_final: 0.7518 (mtp85)
REVERT: A  280 MET cc_start: 0.7944 (ppp) cc_final: 0.7525 (ppp)
REVERT: A  310 LYS cc_start: 0.6832 (tppt) cc_final: 0.6438 (tppt)
REVERT: A  472 LEU cc_start: 0.8964 (tp) cc_final: 0.8597 (tp)
REVERT: D  103 GLU cc_start: 0.8617 (pt0) cc_final: 0.8285 (pp20)
REVERT: D  106 ARG cc_start: 0.8032 (mmp-170) cc_final: 0.7718 (tmt170)
REVERT: D  124 PHE cc_start: 0.9116 (p90) cc_final: 0.8848 (p90)
REVERT: D  146 ILE cc_start: 0.8960 (mm) cc_final: 0.8684 (mm)
REVERT: D  197 MET cc_start: 0.8475 (mmm) cc_final: 0.8165 (mmp)
REVERT: D  280 MET cc_start: 0.7036 (ppp) cc_final: 0.6694 (tpp)
REVERT: D  283 LEU cc_start: 0.7033 (pp) cc_final: 0.6832 (pp)
REVERT: D  443 ARG cc_start: 0.8847 (ttp-170) cc_final: 0.8065 (mmm160)
REVERT: D  472 LEU cc_start: 0.9239 (tp) cc_final: 0.8944 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2393
  time to fit residues: 48.5850
Evaluate side-chains
  114 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0270
   chunk 24 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 81 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.8842

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

Flipped N/Q/H residues before XYZ refinement:
A 115 GLN
A 314 GLN
D 115 GLN
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 336 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.132378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.101882 restraints weight = 30432.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.105513 restraints weight = 15979.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.107837 restraints weight = 10366.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8988  Z= 0.173
  Angle     :  0.604   6.952  12400  Z= 0.334
  Chirality :  0.040   0.183   1400
  Planarity :  0.004   0.037   1348
  Dihedral  : 24.687 177.716   1688
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  5.38 %
    Favored  : 94.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.52 (0.27), residues: 908
  helix: -0.10 (0.24), residues: 456
  sheet: -1.41 (0.67), residues: 54
  loop : -2.02 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 400 
 HIS   0.003   0.001   HIS D 307 
 PHE   0.034   0.002   PHE D 102 
 TYR   0.012   0.001   TYR A 288 
 ARG   0.003   0.000   ARG A 106 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 1.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8781 (tp) cc_final: 0.8576 (tt)
REVERT: A   36 LEU cc_start: 0.9027 (mp) cc_final: 0.8819 (mp)
REVERT: A  115 GLN cc_start: 0.6679 (tp-100) cc_final: 0.6267 (tp-100)
REVERT: A  176 ARG cc_start: 0.8576 (mtp85) cc_final: 0.7654 (mtp85)
REVERT: A  233 GLU cc_start: 0.6633 (mp0) cc_final: 0.6372 (tm-30)
REVERT: A  280 MET cc_start: 0.7611 (ppp) cc_final: 0.7156 (ppp)
REVERT: A  310 LYS cc_start: 0.7020 (tppt) cc_final: 0.6745 (tppt)
REVERT: A  337 ASP cc_start: 0.4972 (m-30) cc_final: 0.4754 (m-30)
REVERT: A  359 GLU cc_start: 0.6737 (mp0) cc_final: 0.5777 (tm-30)
REVERT: A  467 ILE cc_start: 0.9422 (mt) cc_final: 0.9168 (tp)
REVERT: D   32 LEU cc_start: 0.8748 (tp) cc_final: 0.8435 (tt)
REVERT: D   36 LEU cc_start: 0.9025 (mp) cc_final: 0.8695 (mp)
REVERT: D  106 ARG cc_start: 0.8004 (mmp-170) cc_final: 0.7737 (tmt170)
REVERT: D  197 MET cc_start: 0.8505 (mmm) cc_final: 0.7946 (mmp)
REVERT: D  280 MET cc_start: 0.7050 (ppp) cc_final: 0.6769 (tpp)
REVERT: D  283 LEU cc_start: 0.6868 (pp) cc_final: 0.6602 (pp)
REVERT: D  443 ARG cc_start: 0.8770 (ttp-170) cc_final: 0.7886 (mmm160)
REVERT: D  464 MET cc_start: 0.8573 (tpp) cc_final: 0.8265 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2951
  time to fit residues: 62.9924
Evaluate side-chains
  113 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 84 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0010
   chunk 31 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    2.7994

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** 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 = 0.4177 r_free = 0.4177 target = 0.126827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.095315 restraints weight = 30971.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.098807 restraints weight = 16353.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.101003 restraints weight = 10712.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8988  Z= 0.278
  Angle     :  0.661   6.436  12400  Z= 0.367
  Chirality :  0.042   0.156   1400
  Planarity :  0.005   0.050   1348
  Dihedral  : 24.510 179.587   1688
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 17.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.55 (0.27), residues: 908
  helix: -0.14 (0.24), residues: 452
  sheet: -1.50 (0.65), residues: 54
  loop : -1.98 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 295 
 HIS   0.005   0.001   HIS D 413 
 PHE   0.025   0.002   PHE D 102 
 TYR   0.019   0.002   TYR D 401 
 ARG   0.004   0.001   ARG A 106 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8908 (tp) cc_final: 0.8444 (tt)
REVERT: A   36 LEU cc_start: 0.9101 (mp) cc_final: 0.8774 (mp)
REVERT: A  106 ARG cc_start: 0.7713 (mmp-170) cc_final: 0.7159 (tmt170)
REVERT: A  115 GLN cc_start: 0.6908 (tp-100) cc_final: 0.6493 (tp-100)
REVERT: A  146 ILE cc_start: 0.9145 (mm) cc_final: 0.8844 (mm)
REVERT: A  163 VAL cc_start: 0.9281 (p) cc_final: 0.9056 (m)
REVERT: A  233 GLU cc_start: 0.6511 (mp0) cc_final: 0.6029 (tm-30)
REVERT: A  280 MET cc_start: 0.7320 (ppp) cc_final: 0.6854 (ppp)
REVERT: A  359 GLU cc_start: 0.6684 (mp0) cc_final: 0.5529 (tm-30)
REVERT: A  464 MET cc_start: 0.8849 (tpp) cc_final: 0.8501 (tpp)
REVERT: A  488 TYR cc_start: 0.5407 (m-10) cc_final: 0.4676 (m-10)
REVERT: D  197 MET cc_start: 0.8641 (mmm) cc_final: 0.8082 (mmp)
REVERT: D  219 MET cc_start: 0.8179 (mmp) cc_final: 0.7913 (mmp)
REVERT: D  280 MET cc_start: 0.6956 (ppp) cc_final: 0.6702 (tpp)
REVERT: D  416 ASP cc_start: 0.8166 (t0) cc_final: 0.7703 (p0)
REVERT: D  443 ARG cc_start: 0.8828 (ttp-170) cc_final: 0.7861 (mmm160)
REVERT: D  464 MET cc_start: 0.8801 (tpp) cc_final: 0.8441 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2241
  time to fit residues: 40.1929
Evaluate side-chains
  103 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 63 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 ASN
D  66 GLN
** D 129 ASN ** 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 = 0.4248 r_free = 0.4248 target = 0.134512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.099492 restraints weight = 29519.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.103161 restraints weight = 16534.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.105569 restraints weight = 11309.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.4167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8988  Z= 0.188
  Angle     :  0.602   6.460  12400  Z= 0.332
  Chirality :  0.040   0.185   1400
  Planarity :  0.004   0.043   1348
  Dihedral  : 24.484 179.794   1688
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.27), residues: 908
  helix:  0.06 (0.24), residues: 458
  sheet: -0.96 (0.72), residues: 54
  loop : -1.87 (0.31), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 400 
 HIS   0.003   0.001   HIS A 408 
 PHE   0.025   0.002   PHE A 365 
 TYR   0.015   0.001   TYR D 401 
 ARG   0.005   0.000   ARG A 106 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8854 (tp) cc_final: 0.8484 (tt)
REVERT: A   36 LEU cc_start: 0.9075 (mp) cc_final: 0.8765 (mp)
REVERT: A  106 ARG cc_start: 0.7733 (mmp-170) cc_final: 0.7303 (tmt170)
REVERT: A  115 GLN cc_start: 0.6846 (tp-100) cc_final: 0.6478 (tp-100)
REVERT: A  163 VAL cc_start: 0.9252 (p) cc_final: 0.9045 (m)
REVERT: A  233 GLU cc_start: 0.6614 (mp0) cc_final: 0.6190 (tm-30)
REVERT: A  280 MET cc_start: 0.7237 (ppp) cc_final: 0.6768 (ppp)
REVERT: A  337 ASP cc_start: 0.5048 (m-30) cc_final: 0.4821 (m-30)
REVERT: A  359 GLU cc_start: 0.6635 (mp0) cc_final: 0.5660 (tm-30)
REVERT: A  488 TYR cc_start: 0.5077 (m-10) cc_final: 0.4537 (m-10)
REVERT: D  161 ASP cc_start: 0.7900 (p0) cc_final: 0.6982 (m-30)
REVERT: D  197 MET cc_start: 0.8683 (mmm) cc_final: 0.8153 (mmp)
REVERT: D  340 THR cc_start: 0.7785 (m) cc_final: 0.7156 (p)
REVERT: D  416 ASP cc_start: 0.8195 (t0) cc_final: 0.7740 (p0)
REVERT: D  439 LYS cc_start: 0.8689 (tttt) cc_final: 0.8475 (ttpt)
REVERT: D  443 ARG cc_start: 0.8775 (ttp-170) cc_final: 0.7854 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.2447
  time to fit residues: 44.5391
Evaluate side-chains
  109 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 43 optimal weight:   20.0000
   chunk 83 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 19 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 74 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 ASN ** 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 = 0.4127 r_free = 0.4127 target = 0.123271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.091942 restraints weight = 31426.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.095214 restraints weight = 16918.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.097252 restraints weight = 11234.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.4180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   8988  Z= 0.353
  Angle     :  0.727   9.023  12400  Z= 0.398
  Chirality :  0.044   0.152   1400
  Planarity :  0.005   0.041   1348
  Dihedral  : 24.438 179.539   1688
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 21.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.94 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.69 (0.26), residues: 908
  helix: -0.33 (0.23), residues: 452
  sheet: -1.46 (0.66), residues: 54
  loop : -1.97 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 295 
 HIS   0.006   0.001   HIS D 413 
 PHE   0.023   0.002   PHE A 365 
 TYR   0.021   0.002   TYR A 288 
 ARG   0.006   0.001   ARG D 100 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.9082 (mp) cc_final: 0.8860 (mp)
REVERT: A  106 ARG cc_start: 0.7748 (mmp-170) cc_final: 0.7066 (tmt170)
REVERT: A  115 GLN cc_start: 0.6895 (tp-100) cc_final: 0.6454 (tp-100)
REVERT: A  146 ILE cc_start: 0.9100 (mm) cc_final: 0.8759 (mm)
REVERT: A  233 GLU cc_start: 0.6583 (mp0) cc_final: 0.6063 (tm-30)
REVERT: A  280 MET cc_start: 0.7459 (ppp) cc_final: 0.6915 (ppp)
REVERT: A  359 GLU cc_start: 0.6719 (mp0) cc_final: 0.5497 (tm-30)
REVERT: A  402 TYR cc_start: 0.6101 (m-80) cc_final: 0.5883 (m-10)
REVERT: A  439 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8356 (ptmt)
REVERT: A  488 TYR cc_start: 0.5108 (m-10) cc_final: 0.4361 (m-10)
REVERT: D  106 ARG cc_start: 0.6514 (tmt170) cc_final: 0.5922 (tmt170)
REVERT: D  116 LEU cc_start: 0.8024 (mt) cc_final: 0.7803 (mt)
REVERT: D  197 MET cc_start: 0.8697 (mmm) cc_final: 0.8120 (mmp)
REVERT: D  402 TYR cc_start: 0.6925 (m-80) cc_final: 0.6651 (m-10)
REVERT: D  416 ASP cc_start: 0.8217 (t0) cc_final: 0.7792 (p0)
REVERT: D  417 ILE cc_start: 0.8618 (tp) cc_final: 0.8418 (tp)
REVERT: D  464 MET cc_start: 0.8989 (tpp) cc_final: 0.8288 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2226
  time to fit residues: 37.2246
Evaluate side-chains
  106 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 67 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 84 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  66 GLN
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.126939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.097173 restraints weight = 29080.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.100656 restraints weight = 15008.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.102978 restraints weight = 9697.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.4623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8988  Z= 0.193
  Angle     :  0.611   5.839  12400  Z= 0.340
  Chirality :  0.040   0.158   1400
  Planarity :  0.005   0.090   1348
  Dihedral  : 24.438 179.843   1688
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.34 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.30 (0.27), residues: 908
  helix: -0.00 (0.24), residues: 450
  sheet: -1.17 (0.67), residues: 52
  loop : -1.80 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 400 
 HIS   0.006   0.001   HIS D 307 
 PHE   0.021   0.002   PHE A 365 
 TYR   0.024   0.002   TYR A  73 
 ARG   0.005   0.001   ARG D 443 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.8573 (tp) cc_final: 0.8363 (tp)
REVERT: A   32 LEU cc_start: 0.8839 (tp) cc_final: 0.8476 (tt)
REVERT: A   36 LEU cc_start: 0.9074 (mp) cc_final: 0.8780 (mp)
REVERT: A  152 VAL cc_start: 0.9320 (t) cc_final: 0.9104 (t)
REVERT: A  233 GLU cc_start: 0.6686 (mp0) cc_final: 0.6145 (tm-30)
REVERT: A  280 MET cc_start: 0.7508 (ppp) cc_final: 0.7003 (ppp)
REVERT: A  310 LYS cc_start: 0.7395 (mmmt) cc_final: 0.6943 (mmtm)
REVERT: A  359 GLU cc_start: 0.6716 (mp0) cc_final: 0.5732 (tm-30)
REVERT: A  376 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7746 (mm-30)
REVERT: A  439 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8222 (ptmt)
REVERT: A  464 MET cc_start: 0.9251 (ttm) cc_final: 0.8678 (ttp)
REVERT: A  488 TYR cc_start: 0.4732 (m-10) cc_final: 0.4106 (m-80)
REVERT: D  106 ARG cc_start: 0.6275 (tmt170) cc_final: 0.5708 (tmt170)
REVERT: D  152 VAL cc_start: 0.9361 (t) cc_final: 0.9144 (t)
REVERT: D  161 ASP cc_start: 0.7453 (p0) cc_final: 0.6736 (m-30)
REVERT: D  197 MET cc_start: 0.8634 (mmm) cc_final: 0.8093 (mmp)
REVERT: D  233 GLU cc_start: 0.6894 (mp0) cc_final: 0.6408 (tm-30)
REVERT: D  402 TYR cc_start: 0.6882 (m-80) cc_final: 0.6541 (m-10)
REVERT: D  416 ASP cc_start: 0.8252 (t0) cc_final: 0.7832 (p0)
REVERT: D  417 ILE cc_start: 0.8482 (tp) cc_final: 0.8276 (tp)
REVERT: D  439 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8377 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2095
  time to fit residues: 40.3354
Evaluate side-chains
  111 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 91 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0060
   chunk 66 optimal weight:    0.0000
   chunk 75 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.2004

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

Flipped N/Q/H residues before XYZ refinement:
** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 HIS
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 408 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.136491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.099874 restraints weight = 30719.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.103710 restraints weight = 17112.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.106263 restraints weight = 11631.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8988  Z= 0.182
  Angle     :  0.590   5.771  12400  Z= 0.328
  Chirality :  0.039   0.147   1400
  Planarity :  0.005   0.094   1348
  Dihedral  : 24.343 178.673   1688
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.61 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.18 (0.28), residues: 908
  helix: -0.00 (0.24), residues: 458
  sheet: -1.02 (0.69), residues: 52
  loop : -1.65 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 295 
 HIS   0.003   0.001   HIS D 413 
 PHE   0.037   0.002   PHE A 102 
 TYR   0.031   0.001   TYR A  73 
 ARG   0.006   0.000   ARG A 106 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8832 (tp) cc_final: 0.8585 (tt)
REVERT: A   36 LEU cc_start: 0.8949 (mp) cc_final: 0.8732 (mp)
REVERT: A  106 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7190 (tmt170)
REVERT: A  219 MET cc_start: 0.8387 (mmp) cc_final: 0.8154 (mmp)
REVERT: A  233 GLU cc_start: 0.6794 (mp0) cc_final: 0.6315 (tm-30)
REVERT: A  280 MET cc_start: 0.7235 (ppp) cc_final: 0.6801 (ppp)
REVERT: A  359 GLU cc_start: 0.6580 (mp0) cc_final: 0.5611 (tm-30)
REVERT: A  439 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8306 (ptmt)
REVERT: A  464 MET cc_start: 0.9263 (ttm) cc_final: 0.8675 (ttp)
REVERT: D  161 ASP cc_start: 0.7715 (p0) cc_final: 0.7046 (m-30)
REVERT: D  197 MET cc_start: 0.8578 (mmm) cc_final: 0.8030 (mmp)
REVERT: D  233 GLU cc_start: 0.6771 (mp0) cc_final: 0.6198 (tm-30)
REVERT: D  340 THR cc_start: 0.7870 (m) cc_final: 0.7551 (m)
REVERT: D  402 TYR cc_start: 0.6954 (m-80) cc_final: 0.6606 (m-10)
REVERT: D  416 ASP cc_start: 0.8332 (t0) cc_final: 0.7912 (p0)
REVERT: D  439 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8376 (ptmt)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2211
  time to fit residues: 40.4928
Evaluate side-chains
  105 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 76 optimal weight:   20.0000
   chunk 39 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.8388

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 129 ASN
D 307 HIS
** D 413 HIS ** 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 = 0.4246 r_free = 0.4246 target = 0.134804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.098562 restraints weight = 30201.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.102209 restraints weight = 16809.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.104652 restraints weight = 11490.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.5138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8988  Z= 0.215
  Angle     :  0.614   6.037  12400  Z= 0.341
  Chirality :  0.041   0.232   1400
  Planarity :  0.005   0.099   1348
  Dihedral  : 24.291 179.467   1688
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.98 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.10 (0.28), residues: 908
  helix:  0.04 (0.24), residues: 460
  sheet: -0.98 (0.71), residues: 52
  loop : -1.57 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 295 
 HIS   0.007   0.001   HIS D 307 
 PHE   0.034   0.002   PHE D 102 
 TYR   0.026   0.002   TYR D  73 
 ARG   0.006   0.001   ARG A 106 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8907 (tp) cc_final: 0.8618 (tt)
REVERT: A   36 LEU cc_start: 0.9010 (mp) cc_final: 0.8765 (mp)
REVERT: A  102 PHE cc_start: 0.8494 (m-80) cc_final: 0.7972 (m-80)
REVERT: A  152 VAL cc_start: 0.9358 (t) cc_final: 0.9149 (t)
REVERT: A  219 MET cc_start: 0.8382 (mmp) cc_final: 0.8154 (mmp)
REVERT: A  280 MET cc_start: 0.7236 (ppp) cc_final: 0.6848 (ppp)
REVERT: A  359 GLU cc_start: 0.6597 (mp0) cc_final: 0.5535 (tm-30)
REVERT: A  439 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8358 (ptmt)
REVERT: A  464 MET cc_start: 0.9236 (ttm) cc_final: 0.8632 (ttp)
REVERT: D  152 VAL cc_start: 0.9376 (t) cc_final: 0.9152 (t)
REVERT: D  161 ASP cc_start: 0.7702 (p0) cc_final: 0.7037 (m-30)
REVERT: D  197 MET cc_start: 0.8569 (mmm) cc_final: 0.8166 (mmp)
REVERT: D  233 GLU cc_start: 0.6602 (mp0) cc_final: 0.6013 (tm-30)
REVERT: D  340 THR cc_start: 0.7999 (m) cc_final: 0.7629 (m)
REVERT: D  402 TYR cc_start: 0.6916 (m-80) cc_final: 0.6572 (m-10)
REVERT: D  416 ASP cc_start: 0.8276 (t0) cc_final: 0.7866 (p0)
REVERT: D  439 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8391 (ptmt)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2177
  time to fit residues: 38.5349
Evaluate side-chains
  101 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 18 optimal weight:    8.9990
   chunk 87 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 ASN ** 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 = 0.4249 r_free = 0.4249 target = 0.133700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.102287 restraints weight = 30964.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.105829 restraints weight = 16090.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.108094 restraints weight = 10426.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.5477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8988  Z= 0.179
  Angle     :  0.604   5.763  12400  Z= 0.335
  Chirality :  0.040   0.187   1400
  Planarity :  0.005   0.088   1348
  Dihedral  : 24.262 179.174   1688
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.98 (0.28), residues: 908
  helix:  0.12 (0.24), residues: 462
  sheet: -0.91 (0.69), residues: 52
  loop : -1.51 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 295 
 HIS   0.003   0.001   HIS D 413 
 PHE   0.032   0.002   PHE A 102 
 TYR   0.031   0.002   TYR A 288 
 ARG   0.004   0.000   ARG D 443 

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8766 (tp) cc_final: 0.8514 (tt)
REVERT: A   36 LEU cc_start: 0.8982 (mp) cc_final: 0.8732 (mp)
REVERT: A  102 PHE cc_start: 0.8613 (m-80) cc_final: 0.8382 (m-80)
REVERT: A  106 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7351 (tmt170)
REVERT: A  163 VAL cc_start: 0.9286 (p) cc_final: 0.9066 (m)
REVERT: A  219 MET cc_start: 0.8490 (mmp) cc_final: 0.8214 (mmp)
REVERT: A  280 MET cc_start: 0.6926 (ppp) cc_final: 0.6535 (ppp)
REVERT: A  319 ASP cc_start: 0.8516 (m-30) cc_final: 0.8090 (p0)
REVERT: A  359 GLU cc_start: 0.6637 (mp0) cc_final: 0.5706 (tm-30)
REVERT: A  439 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8272 (ptmt)
REVERT: A  446 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8490 (tp30)
REVERT: A  464 MET cc_start: 0.9326 (ttm) cc_final: 0.8709 (ttp)
REVERT: D  161 ASP cc_start: 0.7669 (p0) cc_final: 0.7123 (m-30)
REVERT: D  197 MET cc_start: 0.8613 (mmm) cc_final: 0.8189 (mmp)
REVERT: D  233 GLU cc_start: 0.6330 (mp0) cc_final: 0.5787 (tm-30)
REVERT: D  340 THR cc_start: 0.7954 (m) cc_final: 0.7595 (m)
REVERT: D  402 TYR cc_start: 0.6992 (m-80) cc_final: 0.6654 (m-10)
REVERT: D  416 ASP cc_start: 0.8303 (t0) cc_final: 0.7865 (p0)
REVERT: D  439 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8308 (ptmt)
REVERT: D  464 MET cc_start: 0.9255 (ttm) cc_final: 0.8563 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2233
  time to fit residues: 39.7752
Evaluate side-chains
  106 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 43 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 HIS
** D 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.132362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.096619 restraints weight = 29519.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.100237 restraints weight = 16420.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.102654 restraints weight = 11134.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.5483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8988  Z= 0.233
  Angle     :  0.635   6.784  12400  Z= 0.351
  Chirality :  0.041   0.196   1400
  Planarity :  0.005   0.089   1348
  Dihedral  : 24.233 179.669   1688
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.37 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.99 (0.28), residues: 908
  helix:  0.11 (0.24), residues: 462
  sheet: -0.97 (0.69), residues: 52
  loop : -1.49 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP D 295 
 HIS   0.008   0.001   HIS D 307 
 PHE   0.031   0.002   PHE D 102 
 TYR   0.034   0.002   TYR A 288 
 ARG   0.005   0.001   ARG D 443 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2979.65 seconds
wall clock time: 54 minutes 0.75 seconds (3240.75 seconds total)