Starting phenix.real_space_refine
on Thu Feb 13 05:49:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pqy_20456/02_2025/6pqy_20456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pqy_20456/02_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_20456/02_2025/6pqy_20456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pqy_20456/02_2025/6pqy_20456.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pqy_20456/02_2025/6pqy_20456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pqy_20456/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.75, per 1000 atoms: 0.66
  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: 2.64
  Conformation dependent library (CDL) restraints added in 831.6 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: 3.39
  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: 3.15

  Time building geometry restraints manager: 2.99 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:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     26.000
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.670
-------------------------------------------------------------------------------
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  : 0.880 
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: 0.2688
  time to fit residues: 51.1747
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  : 0.876 
-------------------------------------------------------------------------------
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 = 0.100907 restraints weight = 29742.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.104549 restraints weight = 15730.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.106894 restraints weight = 10167.332|
|-----------------------------------------------------------------------------|
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  : 0.882 
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: 0.8318 (tp)
REVERT: A   32 LEU cc_start: 0.8842 (tp) cc_final: 0.8568 (tt)
REVERT: A  103 GLU cc_start: 0.8741 (pt0) cc_final: 0.8418 (pp20)
REVERT: A  106 ARG cc_start: 0.7592 (mmp-170) cc_final: 0.7046 (tmt170)
REVERT: A  115 GLN cc_start: 0.6722 (tp40) cc_final: 0.6103 (tp-100)
REVERT: A  124 PHE cc_start: 0.8992 (p90) cc_final: 0.8773 (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: 0.6833 (tppt) cc_final: 0.6439 (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: 0.7719 (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: 0.8683 (mm)
REVERT: D  197 MET cc_start: 0.8475 (mmm) cc_final: 0.8164 (mmp)
REVERT: D  280 MET cc_start: 0.7037 (ppp) cc_final: 0.6695 (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: 0.9240 (tp) cc_final: 0.8945 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2463
  time to fit residues: 49.6892
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  : 0.851 
-------------------------------------------------------------------------------
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:    0.0170
   chunk 24 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 81 optimal weight:    9.9990
   chunk 78 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.9824

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.132056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.101333 restraints weight = 30635.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.105009 restraints weight = 15990.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.107321 restraints weight = 10352.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.3283

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= 0.176
  Angle     :  0.608   6.752  12400  Z= 0.336
  Chirality :  0.040   0.181   1400
  Planarity :  0.004   0.037   1348
  Dihedral  : 24.717 177.817   1688
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  5.01 %
    Favored  : 94.87 %
  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: -1.59 (0.27), residues: 908
  helix: -0.16 (0.23), residues: 456
  sheet: -1.43 (0.66), residues: 54
  loop : -2.05 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 400 
 HIS   0.003   0.001   HIS D 307 
 PHE   0.035   0.002   PHE D 102 
 TYR   0.012   0.001   TYR A 402 
 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
  153 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8786 (tp) cc_final: 0.8579 (tt)
REVERT: A   36 LEU cc_start: 0.9031 (mp) cc_final: 0.8820 (mp)
REVERT: A  115 GLN cc_start: 0.6783 (tp-100) cc_final: 0.6319 (tp-100)
REVERT: A  176 ARG cc_start: 0.8586 (mtp85) cc_final: 0.7786 (mtp85)
REVERT: A  233 GLU cc_start: 0.6731 (mp0) cc_final: 0.6403 (tm-30)
REVERT: A  280 MET cc_start: 0.7595 (ppp) cc_final: 0.7152 (ppp)
REVERT: A  310 LYS cc_start: 0.7010 (tppt) cc_final: 0.6738 (tppt)
REVERT: A  359 GLU cc_start: 0.6695 (mp0) cc_final: 0.5705 (tm-30)
REVERT: A  467 ILE cc_start: 0.9437 (mt) cc_final: 0.9179 (tp)
REVERT: D  106 ARG cc_start: 0.8010 (mmp-170) cc_final: 0.7689 (tmt170)
REVERT: D  197 MET cc_start: 0.8522 (mmm) cc_final: 0.7970 (mmp)
REVERT: D  280 MET cc_start: 0.6995 (ppp) cc_final: 0.6728 (tpp)
REVERT: D  283 LEU cc_start: 0.6965 (pp) cc_final: 0.6703 (pp)
REVERT: D  443 ARG cc_start: 0.8806 (ttp-170) cc_final: 0.7918 (mmm160)
REVERT: D  464 MET cc_start: 0.8583 (tpp) cc_final: 0.8242 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2238
  time to fit residues: 45.9115
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  : 0.922 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 23 optimal weight:    0.4980
   chunk 84 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN
A 336 ASN
** D 129 ASN ** 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 = 0.4231 r_free = 0.4231 target = 0.130552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.099228 restraints weight = 30708.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.102799 restraints weight = 16479.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.105068 restraints weight = 10825.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.3746

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= 0.208
  Angle     :  0.609   6.091  12400  Z= 0.339
  Chirality :  0.041   0.149   1400
  Planarity :  0.004   0.052   1348
  Dihedral  : 24.524 179.071   1688
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  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: -1.41 (0.27), residues: 908
  helix: -0.06 (0.24), residues: 456
  sheet: -1.57 (0.69), residues: 50
  loop : -1.87 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 400 
 HIS   0.004   0.001   HIS D 413 
 PHE   0.026   0.002   PHE D 102 
 TYR   0.011   0.001   TYR A 288 
 ARG   0.006   0.001   ARG A 100 

*********************** 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
  143 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8795 (tp) cc_final: 0.8446 (tt)
REVERT: A   36 LEU cc_start: 0.9039 (mp) cc_final: 0.8758 (mp)
REVERT: A  115 GLN cc_start: 0.6889 (tp-100) cc_final: 0.6526 (tp-100)
REVERT: A  146 ILE cc_start: 0.9176 (mm) cc_final: 0.8903 (mm)
REVERT: A  233 GLU cc_start: 0.6469 (mp0) cc_final: 0.5990 (tm-30)
REVERT: A  280 MET cc_start: 0.7270 (ppp) cc_final: 0.6792 (ppp)
REVERT: A  319 ASP cc_start: 0.8504 (m-30) cc_final: 0.8043 (p0)
REVERT: A  359 GLU cc_start: 0.6676 (mp0) cc_final: 0.5579 (tm-30)
REVERT: A  488 TYR cc_start: 0.5408 (m-80) cc_final: 0.4735 (m-10)
REVERT: D   30 LEU cc_start: 0.9069 (tp) cc_final: 0.8681 (tp)
REVERT: D  106 ARG cc_start: 0.8091 (mmp-170) cc_final: 0.7823 (tmt170)
REVERT: D  152 VAL cc_start: 0.9331 (t) cc_final: 0.9114 (t)
REVERT: D  161 ASP cc_start: 0.7932 (p0) cc_final: 0.6873 (m-30)
REVERT: D  197 MET cc_start: 0.8630 (mmm) cc_final: 0.8084 (mmp)
REVERT: D  219 MET cc_start: 0.8413 (mmp) cc_final: 0.8134 (mmp)
REVERT: D  416 ASP cc_start: 0.8096 (t0) cc_final: 0.7684 (p0)
REVERT: D  443 ARG cc_start: 0.8826 (ttp-170) cc_final: 0.7885 (mmm160)
REVERT: D  464 MET cc_start: 0.8789 (tpp) cc_final: 0.8341 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2201
  time to fit residues: 43.1527
Evaluate side-chains
  108 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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**
D  66 GLN
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 336 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.131389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.100986 restraints weight = 30013.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.104571 restraints weight = 16014.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.106944 restraints weight = 10539.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.4274

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= 0.172
  Angle     :  0.584   6.858  12400  Z= 0.320
  Chirality :  0.040   0.141   1400
  Planarity :  0.004   0.040   1348
  Dihedral  : 24.493 178.777   1688
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  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: -1.01 (0.28), residues: 908
  helix:  0.19 (0.24), residues: 460
  sheet: -0.72 (0.64), residues: 64
  loop : -1.70 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 400 
 HIS   0.002   0.001   HIS D 216 
 PHE   0.024   0.002   PHE A 365 
 TYR   0.014   0.001   TYR A 288 
 ARG   0.004   0.000   ARG D 342 

*********************** 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
  135 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8825 (tp) cc_final: 0.8456 (tt)
REVERT: A   36 LEU cc_start: 0.9033 (mp) cc_final: 0.8786 (mp)
REVERT: A  115 GLN cc_start: 0.6747 (tp-100) cc_final: 0.6484 (tp-100)
REVERT: A  176 ARG cc_start: 0.8572 (mtp85) cc_final: 0.7740 (mtp85)
REVERT: A  233 GLU cc_start: 0.6517 (mp0) cc_final: 0.6048 (tm-30)
REVERT: A  280 MET cc_start: 0.7214 (ppp) cc_final: 0.6738 (ppp)
REVERT: A  310 LYS cc_start: 0.7024 (tppt) cc_final: 0.6525 (pptt)
REVERT: A  359 GLU cc_start: 0.6721 (mp0) cc_final: 0.5790 (tm-30)
REVERT: A  439 LYS cc_start: 0.8444 (tttt) cc_final: 0.8020 (ptmt)
REVERT: A  488 TYR cc_start: 0.5065 (m-80) cc_final: 0.4468 (m-80)
REVERT: D  116 LEU cc_start: 0.8209 (mt) cc_final: 0.7999 (mt)
REVERT: D  197 MET cc_start: 0.8613 (mmm) cc_final: 0.8202 (mmp)
REVERT: D  416 ASP cc_start: 0.8178 (t0) cc_final: 0.7723 (p0)
REVERT: D  443 ARG cc_start: 0.8746 (ttp-170) cc_final: 0.7842 (mmm160)
REVERT: D  464 MET cc_start: 0.8667 (tpp) cc_final: 0.8324 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2240
  time to fit residues: 41.5096
Evaluate side-chains
  104 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
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:    0.0070
   chunk 83 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    0.9804

-------------------------------------------------------------------------------
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 = 0.4268 r_free = 0.4268 target = 0.133515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.102331 restraints weight = 30621.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.105931 restraints weight = 16554.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.108290 restraints weight = 10948.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.4667

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= 0.170
  Angle     :  0.571   5.728  12400  Z= 0.314
  Chirality :  0.039   0.141   1400
  Planarity :  0.004   0.040   1348
  Dihedral  : 24.439 177.663   1688
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  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: -0.87 (0.28), residues: 908
  helix:  0.32 (0.24), residues: 460
  sheet: -0.67 (0.64), residues: 64
  loop : -1.63 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 295 
 HIS   0.003   0.001   HIS A 408 
 PHE   0.031   0.001   PHE A 102 
 TYR   0.020   0.001   TYR D  73 
 ARG   0.004   0.000   ARG A 106 

*********************** 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
  136 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8856 (tp) cc_final: 0.8569 (tt)
REVERT: A   36 LEU cc_start: 0.8991 (mp) cc_final: 0.8754 (mp)
REVERT: A  106 ARG cc_start: 0.8074 (mmp-170) cc_final: 0.7134 (tmt170)
REVERT: A  115 GLN cc_start: 0.6718 (tp-100) cc_final: 0.6500 (tp-100)
REVERT: A  233 GLU cc_start: 0.6504 (mp0) cc_final: 0.5995 (tm-30)
REVERT: A  280 MET cc_start: 0.7228 (ppp) cc_final: 0.6749 (ppp)
REVERT: A  291 ASP cc_start: 0.8265 (t0) cc_final: 0.8043 (t0)
REVERT: A  310 LYS cc_start: 0.7413 (tppt) cc_final: 0.6713 (pptt)
REVERT: A  359 GLU cc_start: 0.6705 (mp0) cc_final: 0.5773 (tm-30)
REVERT: A  439 LYS cc_start: 0.8536 (tttt) cc_final: 0.8118 (ptmt)
REVERT: A  464 MET cc_start: 0.8759 (tpp) cc_final: 0.8208 (tpp)
REVERT: A  488 TYR cc_start: 0.4981 (m-80) cc_final: 0.4405 (m-10)
REVERT: D  103 GLU cc_start: 0.8366 (pt0) cc_final: 0.8163 (pt0)
REVERT: D  176 ARG cc_start: 0.8713 (mtp85) cc_final: 0.7716 (mtp85)
REVERT: D  197 MET cc_start: 0.8515 (mmm) cc_final: 0.8108 (mmp)
REVERT: D  233 GLU cc_start: 0.6712 (mp0) cc_final: 0.6301 (tm-30)
REVERT: D  416 ASP cc_start: 0.8201 (t0) cc_final: 0.7775 (p0)
REVERT: D  417 ILE cc_start: 0.8503 (tp) cc_final: 0.8301 (tp)
REVERT: D  439 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8135 (ptmt)
REVERT: D  443 ARG cc_start: 0.8670 (ttp-170) cc_final: 0.7857 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2372
  time to fit residues: 43.0641
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  : 0.966 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 84 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A 463 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 = 0.4251 r_free = 0.4251 target = 0.133671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.101354 restraints weight = 30063.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.105142 restraints weight = 15702.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.107554 restraints weight = 10205.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.4989

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= 0.161
  Angle     :  0.566   5.775  12400  Z= 0.312
  Chirality :  0.039   0.164   1400
  Planarity :  0.004   0.064   1348
  Dihedral  : 24.377 177.830   1688
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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: -0.71 (0.28), residues: 908
  helix:  0.42 (0.24), residues: 460
  sheet: -0.54 (0.63), residues: 64
  loop : -1.54 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 400 
 HIS   0.003   0.001   HIS D 307 
 PHE   0.031   0.001   PHE D 102 
 TYR   0.021   0.001   TYR D  73 
 ARG   0.005   0.000   ARG A 106 

*********************** 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
  145 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8824 (tp) cc_final: 0.8543 (tt)
REVERT: A   36 LEU cc_start: 0.8963 (mp) cc_final: 0.8742 (mp)
REVERT: A  106 ARG cc_start: 0.8252 (mmp-170) cc_final: 0.7748 (mmm160)
REVERT: A  176 ARG cc_start: 0.8700 (mtp85) cc_final: 0.7822 (mtp85)
REVERT: A  219 MET cc_start: 0.8210 (mmp) cc_final: 0.7903 (mmp)
REVERT: A  233 GLU cc_start: 0.6576 (mp0) cc_final: 0.6102 (tm-30)
REVERT: A  280 MET cc_start: 0.7164 (ppp) cc_final: 0.6845 (tpp)
REVERT: A  310 LYS cc_start: 0.7633 (tppt) cc_final: 0.6912 (pptt)
REVERT: A  359 GLU cc_start: 0.6691 (mp0) cc_final: 0.5778 (tm-30)
REVERT: A  376 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7776 (mm-30)
REVERT: A  439 LYS cc_start: 0.8479 (tttt) cc_final: 0.8054 (ptmt)
REVERT: A  464 MET cc_start: 0.8813 (tpp) cc_final: 0.7928 (tpp)
REVERT: D  103 GLU cc_start: 0.8365 (pt0) cc_final: 0.8143 (pt0)
REVERT: D  176 ARG cc_start: 0.8750 (mtp85) cc_final: 0.7750 (mtp85)
REVERT: D  197 MET cc_start: 0.8565 (mmm) cc_final: 0.8179 (mmp)
REVERT: D  233 GLU cc_start: 0.6811 (mp0) cc_final: 0.6258 (tm-30)
REVERT: D  416 ASP cc_start: 0.8214 (t0) cc_final: 0.7804 (p0)
REVERT: D  439 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8160 (ptmt)
REVERT: D  443 ARG cc_start: 0.8693 (ttp-170) cc_final: 0.7901 (mmm160)
REVERT: D  464 MET cc_start: 0.8930 (tpp) cc_final: 0.8051 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2474
  time to fit residues: 47.4172
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  : 0.921 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 77 optimal weight:    0.6980
   chunk 89 optimal weight:    6.9990
   chunk 32 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   chunk 66 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    2.4186

-------------------------------------------------------------------------------
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
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 129 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 = 0.4197 r_free = 0.4197 target = 0.128247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.096578 restraints weight = 30887.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.100069 restraints weight = 16257.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.102303 restraints weight = 10648.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.4839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8988  Z= 0.252
  Angle     :  0.628   6.401  12400  Z= 0.344
  Chirality :  0.040   0.149   1400
  Planarity :  0.005   0.057   1348
  Dihedral  : 24.296 179.418   1688
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  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: -0.97 (0.28), residues: 908
  helix:  0.14 (0.24), residues: 464
  sheet: -0.78 (0.60), residues: 64
  loop : -1.55 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 400 
 HIS   0.004   0.001   HIS D 413 
 PHE   0.032   0.002   PHE A 102 
 TYR   0.028   0.002   TYR D  73 
 ARG   0.004   0.001   ARG A 309 

*********************** 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
  131 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.8920 (tp) cc_final: 0.8620 (tt)
REVERT: A   36 LEU cc_start: 0.8993 (mp) cc_final: 0.8754 (mp)
REVERT: A  219 MET cc_start: 0.8386 (mmp) cc_final: 0.8152 (mmp)
REVERT: A  233 GLU cc_start: 0.6525 (mp0) cc_final: 0.6057 (tm-30)
REVERT: A  280 MET cc_start: 0.7273 (ppp) cc_final: 0.6746 (ppp)
REVERT: A  310 LYS cc_start: 0.7490 (tppt) cc_final: 0.6855 (pptt)
REVERT: A  359 GLU cc_start: 0.6676 (mp0) cc_final: 0.5625 (tm-30)
REVERT: A  376 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7578 (mm-30)
REVERT: A  439 LYS cc_start: 0.8608 (tttt) cc_final: 0.8175 (ptmt)
REVERT: A  464 MET cc_start: 0.8825 (tpp) cc_final: 0.7864 (tpp)
REVERT: D  106 ARG cc_start: 0.6320 (tmt170) cc_final: 0.5774 (tmt170)
REVERT: D  161 ASP cc_start: 0.7442 (p0) cc_final: 0.6775 (m-30)
REVERT: D  197 MET cc_start: 0.8632 (mmm) cc_final: 0.8041 (mmp)
REVERT: D  219 MET cc_start: 0.8430 (mmp) cc_final: 0.8207 (mmp)
REVERT: D  233 GLU cc_start: 0.6864 (mp0) cc_final: 0.6312 (tm-30)
REVERT: D  402 TYR cc_start: 0.6707 (m-80) cc_final: 0.6507 (m-10)
REVERT: D  416 ASP cc_start: 0.8303 (t0) cc_final: 0.7882 (p0)
REVERT: D  439 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8343 (ptmt)
REVERT: D  443 ARG cc_start: 0.8785 (ttp-170) cc_final: 0.7894 (mmm160)
REVERT: D  464 MET cc_start: 0.9011 (tpp) cc_final: 0.8115 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2208
  time to fit residues: 39.5236
Evaluate side-chains
  107 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 83 optimal weight:    8.9990
   chunk 3 optimal weight:    0.6980
   chunk 94 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0270
   chunk 76 optimal weight:    0.0070
   chunk 39 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A 463 ASN
** D 129 ASN ** 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 = 0.4298 r_free = 0.4298 target = 0.137016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.106416 restraints weight = 30396.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.110069 restraints weight = 15771.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.112407 restraints weight = 10160.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.5339

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= 0.162
  Angle     :  0.585   6.126  12400  Z= 0.318
  Chirality :  0.039   0.145   1400
  Planarity :  0.004   0.053   1348
  Dihedral  : 24.282 178.924   1688
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.49 %
    Favored  : 99.39 %
  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: -0.76 (0.28), residues: 908
  helix:  0.27 (0.24), residues: 468
  sheet: -0.49 (0.60), residues: 64
  loop : -1.45 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 400 
 HIS   0.002   0.000   HIS A 216 
 PHE   0.031   0.002   PHE A 102 
 TYR   0.034   0.001   TYR D  73 
 ARG   0.005   0.000   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
  153 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.930 
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: 0.8769 (tp) cc_final: 0.8558 (tt)
REVERT: A   36 LEU cc_start: 0.8945 (mp) cc_final: 0.8723 (mp)
REVERT: A   71 GLN cc_start: 0.9132 (mm110) cc_final: 0.8741 (tp40)
REVERT: A  102 PHE cc_start: 0.8540 (m-80) cc_final: 0.7906 (m-80)
REVERT: A  176 ARG cc_start: 0.8724 (mtp85) cc_final: 0.7899 (mtp85)
REVERT: A  219 MET cc_start: 0.8319 (mmp) cc_final: 0.8069 (mmp)
REVERT: A  233 GLU cc_start: 0.6470 (mp0) cc_final: 0.6146 (tm-30)
REVERT: A  280 MET cc_start: 0.7114 (ppp) cc_final: 0.6727 (tpt)
REVERT: A  310 LYS cc_start: 0.7685 (tppt) cc_final: 0.6954 (pptt)
REVERT: A  319 ASP cc_start: 0.8555 (m-30) cc_final: 0.8123 (p0)
REVERT: A  359 GLU cc_start: 0.6798 (mp0) cc_final: 0.5927 (tm-30)
REVERT: A  376 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7716 (mm-30)
REVERT: A  439 LYS cc_start: 0.8472 (tttt) cc_final: 0.8018 (ptmt)
REVERT: A  464 MET cc_start: 0.8812 (tpp) cc_final: 0.7937 (tpp)
REVERT: D  161 ASP cc_start: 0.7158 (p0) cc_final: 0.6643 (m-30)
REVERT: D  176 ARG cc_start: 0.8654 (mtp85) cc_final: 0.7701 (mtp85)
REVERT: D  197 MET cc_start: 0.8530 (mmm) cc_final: 0.8152 (mmp)
REVERT: D  219 MET cc_start: 0.8397 (mmp) cc_final: 0.8143 (mmp)
REVERT: D  233 GLU cc_start: 0.6483 (mp0) cc_final: 0.5937 (tm-30)
REVERT: D  416 ASP cc_start: 0.8275 (t0) cc_final: 0.7859 (p0)
REVERT: D  417 ILE cc_start: 0.8479 (tp) cc_final: 0.8277 (tp)
REVERT: D  426 ILE cc_start: 0.7169 (mm) cc_final: 0.6953 (tp)
REVERT: D  439 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8186 (ptmt)
REVERT: D  443 ARG cc_start: 0.8690 (ttp-170) cc_final: 0.7912 (mmm160)
REVERT: D  464 MET cc_start: 0.8842 (tpp) cc_final: 0.7994 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2442
  time to fit residues: 49.2557
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  : 0.899 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 52 optimal weight:    0.0570
   chunk 18 optimal weight:   10.0000
   chunk 87 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 77 optimal weight:    0.2980
   chunk 76 optimal weight:   20.0000
   chunk 53 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 458 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.128999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.099806 restraints weight = 28680.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.103295 restraints weight = 15160.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.105542 restraints weight = 9840.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.5592

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= 0.168
  Angle     :  0.575   5.966  12400  Z= 0.312
  Chirality :  0.038   0.146   1400
  Planarity :  0.004   0.049   1348
  Dihedral  : 24.230 177.525   1688
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.00 %
    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: -0.69 (0.28), residues: 908
  helix:  0.34 (0.24), residues: 468
  sheet: -0.38 (0.59), residues: 64
  loop : -1.45 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 400 
 HIS   0.002   0.001   HIS D 285 
 PHE   0.028   0.001   PHE A 102 
 TYR   0.031   0.001   TYR D  73 
 ARG   0.004   0.000   ARG A 106 

********************** 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
  146 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.825 
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   36 LEU cc_start: 0.8950 (mp) cc_final: 0.8707 (mp)
REVERT: A   71 GLN cc_start: 0.9138 (mm110) cc_final: 0.8732 (tp40)
REVERT: A  219 MET cc_start: 0.8463 (mmp) cc_final: 0.8225 (mmp)
REVERT: A  280 MET cc_start: 0.7105 (ppp) cc_final: 0.6785 (tpt)
REVERT: A  310 LYS cc_start: 0.7686 (tppt) cc_final: 0.6959 (pptt)
REVERT: A  319 ASP cc_start: 0.8539 (m-30) cc_final: 0.8125 (p0)
REVERT: A  359 GLU cc_start: 0.6788 (mp0) cc_final: 0.5918 (tm-30)
REVERT: A  439 LYS cc_start: 0.8451 (tttt) cc_final: 0.8026 (ptmt)
REVERT: A  464 MET cc_start: 0.8851 (tpp) cc_final: 0.8015 (tpp)
REVERT: D  103 GLU cc_start: 0.8560 (pt0) cc_final: 0.8273 (pp20)
REVERT: D  106 ARG cc_start: 0.6289 (tmt170) cc_final: 0.5877 (tmt170)
REVERT: D  161 ASP cc_start: 0.7471 (p0) cc_final: 0.6985 (m-30)
REVERT: D  176 ARG cc_start: 0.8822 (mtp85) cc_final: 0.7868 (mtp85)
REVERT: D  197 MET cc_start: 0.8544 (mmm) cc_final: 0.8159 (mmp)
REVERT: D  219 MET cc_start: 0.8558 (mmp) cc_final: 0.8321 (mmp)
REVERT: D  416 ASP cc_start: 0.8267 (t0) cc_final: 0.7859 (p0)
REVERT: D  426 ILE cc_start: 0.7090 (mm) cc_final: 0.6868 (tp)
REVERT: D  439 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8138 (ptmt)
REVERT: D  443 ARG cc_start: 0.8733 (ttp-170) cc_final: 0.7934 (mmm160)
REVERT: D  464 MET cc_start: 0.8954 (tpp) cc_final: 0.8045 (tpp)
REVERT: D  472 LEU cc_start: 0.9186 (tp) cc_final: 0.8861 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2464
  time to fit residues: 47.5706
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  : 0.894 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 43 optimal weight:    0.3980
   chunk 22 optimal weight:   20.0000
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
D 129 ASN
D 307 HIS
** D 463 ASN ** 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 = 0.4257 r_free = 0.4257 target = 0.128812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.099588 restraints weight = 28820.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.103003 restraints weight = 15344.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.105143 restraints weight = 10074.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.5727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8988  Z= 0.178
  Angle     :  0.586   8.307  12400  Z= 0.315
  Chirality :  0.038   0.134   1400
  Planarity :  0.004   0.046   1348
  Dihedral  : 24.182 178.202   1688
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.00 %
    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: -0.67 (0.28), residues: 908
  helix:  0.30 (0.24), residues: 468
  sheet: -0.25 (0.59), residues: 64
  loop : -1.39 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 400 
 HIS   0.008   0.001   HIS D 307 
 PHE   0.016   0.001   PHE A 365 
 TYR   0.029   0.001   TYR D  73 
 ARG   0.004   0.000   ARG A 106 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2885.76 seconds
wall clock time: 52 minutes 43.42 seconds (3163.42 seconds total)