Starting phenix.real_space_refine
on Wed Jul 30 04:31:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f12_50122/07_2025/9f12_50122.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f12_50122/07_2025/9f12_50122.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f12_50122/07_2025/9f12_50122.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f12_50122/07_2025/9f12_50122.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f12_50122/07_2025/9f12_50122.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f12_50122/07_2025/9f12_50122.cif"
  }
  resolution = 3.42
  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=   0.001 sd=   0.042
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: 6
    Type Number    sf(0)   Gaussians
     P     181      5.49       5
     Mg      1      5.21       5
     S      35      5.16       5
     C    7049      2.51       5
     N    2214      2.21       5
     O    2691      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12171
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 1982
          Classifications: {'DNA': 96}
          Link IDs: {'rna3p': 95}
    Chain: "B"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1739
          Classifications: {'DNA': 85}
          Link IDs: {'rna3p': 84}
    Chain: "C"
      Number of atoms: 764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 764
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 5, 'TRANS': 89}
    Chain: "D"
      Number of atoms: 749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 749
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 88}
    Chain: "F"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 960
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 846
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 881
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 881
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 105}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "H"
      Number of atoms: 4249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 564, 4249
          Classifications: {'peptide': 564}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 22, 'TRANS': 541}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 129
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 6, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 69
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 10.60, per 1000 atoms: 0.87
  Number of scatterers: 12171
  At special positions: 0
  Unit cell: (94.875, 130.35, 181.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      35     16.00
     P     181     15.00
     Mg      1     11.99
     O    2691      8.00
     N    2214      7.00
     C    7049      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: 2.82
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2034

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 14 sheets defined
      45.6% alpha, 17.8% beta
      81 base pairs and 154 stacking pairs defined.
    Time for finding SS restraints: 5.33
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 16
    Processing helix  chain 'C' and resid 19 through 40
      removed outlier: 3.708A  pdb=" N   ILE C  34 " --> pdb=" O   PHE C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 84 through 92
    Processing helix  chain 'D' and resid 2 through 14
    Processing helix  chain 'D' and resid 18 through 39
    Processing helix  chain 'D' and resid 83 through 91
    Processing helix  chain 'F' and resid 22 through 34
      removed outlier: 3.743A  pdb=" N   LEU F  26 " --> pdb=" O   VAL F  22 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 36 through 52
      removed outlier: 3.712A  pdb=" N   ALA F  41 " --> pdb=" O   ARG F  37 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   HIS F  50 " --> pdb=" O   LYS F  46 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 75 through 90
      removed outlier: 3.651A  pdb=" N   GLN F  80 " --> pdb=" O   ASP F  76 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 108
    Processing helix  chain 'G' and resid 20 through 34
      removed outlier: 4.408A  pdb=" N   LEU G  25 " --> pdb=" O   ASP G  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 52
    Processing helix  chain 'G' and resid 75 through 90
      removed outlier: 3.597A  pdb=" N   ALA G  84 " --> pdb=" O   GLN G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 108
      removed outlier: 4.010A  pdb=" N   ARG G 100 " --> pdb=" O   GLU G  96 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 32
      removed outlier: 3.756A  pdb=" N   SER E  24 " --> pdb=" O   VAL E  20 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LEU E  25 " --> pdb=" O   ASP E  21 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 36 through 52
      removed outlier: 3.621A  pdb=" N   HIS E  50 " --> pdb=" O   LYS E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 75 through 90
      removed outlier: 3.545A  pdb=" N   LEU E  81 " --> pdb=" O   GLU E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 108
    Processing helix  chain 'H' and resid 9 through 18
      removed outlier: 3.611A  pdb=" N   ALA H  13 " --> pdb=" O   SER H   9 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR H  18 " --> pdb=" O   GLY H  14 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 35 through 41
    Processing helix  chain 'H' and resid 48 through 58
    Processing helix  chain 'H' and resid 87 through 98
    Processing helix  chain 'H' and resid 99 through 118
      removed outlier: 3.510A  pdb=" N   ILE H 103 " --> pdb=" O   ASP H  99 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 184 through 192
    Processing helix  chain 'H' and resid 192 through 211
    Processing helix  chain 'H' and resid 219 through 222
      removed outlier: 3.567A  pdb=" N   GLY H 222 " --> pdb=" O   GLY H 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 219 through 222'
    Processing helix  chain 'H' and resid 229 through 233
    Processing helix  chain 'H' and resid 235 through 246
    Processing helix  chain 'H' and resid 250 through 261
    Processing helix  chain 'H' and resid 269 through 283
      removed outlier: 3.636A  pdb=" N   LYS H 282 " --> pdb=" O   MET H 278 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 287 through 302
      removed outlier: 3.762A  pdb=" N   ASP H 300 " --> pdb=" O   ASP H 296 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU H 301 " --> pdb=" O   GLN H 297 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 575 through 593
    Processing helix  chain 'H' and resid 603 through 621
      removed outlier: 3.613A  pdb=" N   ALA H 613 " --> pdb=" O   ILE H 609 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 646 through 650
    Processing helix  chain 'H' and resid 696 through 698
      No H-bonds generated for 'chain 'H' and resid 696 through 698'
    Processing helix  chain 'H' and resid 763 through 767
    Processing helix  chain 'H' and resid 798 through 806
    Processing helix  chain 'H' and resid 822 through 827
    Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46
      removed outlier: 3.645A  pdb=" N   VAL C  44 " --> pdb=" O   PHE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 45
    Processing sheet with id=AA3, first strand: chain 'D' and resid 59 through 62
    Processing sheet with id=AA4, first strand: chain 'F' and resid 13 through 19
      removed outlier: 3.582A  pdb=" N   LEU F  18 " --> pdb=" O   LYS F  68 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 13 through 19
    Processing sheet with id=AA6, first strand: chain 'E' and resid 13 through 19
    Processing sheet with id=AA7, first strand: chain 'H' and resid 2 through 7
      removed outlier: 4.051A  pdb=" N   GLY H  79 " --> pdb=" O   VAL H   7 " (cutoff:3.500A)
      removed outlier: 5.565A  pdb=" N   GLN H 155 " --> pdb=" O   THR H 148 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   THR H 148 " --> pdb=" O   GLN H 155 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 69 through 70
    Processing sheet with id=AA9, first strand: chain 'H' and resid 122 through 126
    Processing sheet with id=AB1, first strand: chain 'H' and resid 166 through 167
    Processing sheet with id=AB2, first strand: chain 'H' and resid 216 through 217
    Processing sheet with id=AB3, first strand: chain 'H' and resid 775 through 776
      removed outlier: 9.038A  pdb=" N   GLU H 776 " --> pdb=" O   SER H 597 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ALA H 599 " --> pdb=" O   GLU H 776 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL H 598 " --> pdb=" O   PHE H 789 " (cutoff:3.500A)
      removed outlier: 7.615A  pdb=" N   SER H 791 " --> pdb=" O   VAL H 598 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   GLN H 600 " --> pdb=" O   SER H 791 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   VAL H 788 " --> pdb=" O   ARG H 813 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   TYR H 815 " --> pdb=" O   VAL H 788 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ALA H 790 " --> pdb=" O   TYR H 815 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   LEU H 814 " --> pdb=" O   PRO H 567 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   THR H 569 " --> pdb=" O   LEU H 814 " (cutoff:3.500A)
      removed outlier: 7.380A  pdb=" N   SER H 816 " --> pdb=" O   THR H 569 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 629 through 636
      removed outlier: 3.543A  pdb=" N   SER H 665 " --> pdb=" O   ASN H 660 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   THR H 682 " --> pdb=" O   ASP H 672 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   VAL H 674 " --> pdb=" O   SER H 680 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   SER H 680 " --> pdb=" O   VAL H 674 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 755 through 759
      removed outlier: 6.985A  pdb=" N   ALA H 744 " --> pdb=" O   VAL H 740 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   VAL H 740 " --> pdb=" O   ALA H 744 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR H 746 " --> pdb=" O   ALA H 738 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN H 736 " --> pdb=" O   VAL H 748 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      181 hydrogen bonds
      358 hydrogen bond angles
      0 basepair planarities
      81 basepair parallelities
      154 stacking parallelities
  Total time for adding SS restraints: 5.42

  Time building geometry restraints manager: 3.41 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: 2481
        1.33 -     1.45: 3591
        1.45 -     1.57: 6264
        1.57 -     1.69: 360
        1.69 -     1.80: 67
  Bond restraints: 12763
  Sorted by residual:
  bond pdb=" N   ASN H 803 "
       pdb=" CA  ASN H 803 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.026 1.27e-02 6.20e+03 4.18e+00
  bond pdb=" N   LEU H 802 "
       pdb=" CA  LEU H 802 "
    ideal  model  delta    sigma   weight residual
    1.459  1.481 -0.022 1.23e-02 6.61e+03 3.22e+00
  bond pdb=" P    DG A   7 "
       pdb=" OP1  DG A   7 "
    ideal  model  delta    sigma   weight residual
    1.480  1.514 -0.034 2.00e-02 2.50e+03 2.84e+00
  bond pdb=" P    DG A   9 "
       pdb=" OP2  DG A   9 "
    ideal  model  delta    sigma   weight residual
    1.480  1.513 -0.033 2.00e-02 2.50e+03 2.64e+00
  bond pdb=" P    DG A   9 "
       pdb=" OP1  DG A   9 "
    ideal  model  delta    sigma   weight residual
    1.480  1.511 -0.031 2.00e-02 2.50e+03 2.45e+00
  ... (remaining 12758 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 17461
        1.60 -     3.20: 518
        3.20 -     4.81: 38
        4.81 -     6.41: 7
        6.41 -     8.01: 3
  Bond angle restraints: 18027
  Sorted by residual:
  angle pdb=" C   THR H 801 "
        pdb=" N   LEU H 802 "
        pdb=" CA  LEU H 802 "
      ideal   model   delta    sigma   weight residual
     120.29  115.05    5.24 1.42e+00 4.96e-01 1.36e+01
  angle pdb=" N   THR H 284 "
        pdb=" CA  THR H 284 "
        pdb=" C   THR H 284 "
      ideal   model   delta    sigma   weight residual
     110.44  106.26    4.18 1.20e+00 6.94e-01 1.22e+01
  angle pdb=" N   ASN H 803 "
        pdb=" CA  ASN H 803 "
        pdb=" C   ASN H 803 "
      ideal   model   delta    sigma   weight residual
     111.75  107.32    4.43 1.28e+00 6.10e-01 1.20e+01
  angle pdb=" O3'  DG A   7 "
        pdb=" P    DG A   6 "
        pdb=" O5'  DG A   6 "
      ideal   model   delta    sigma   weight residual
     104.00   99.14    4.86 1.50e+00 4.44e-01 1.05e+01
  angle pdb=" N   LEU H 802 "
        pdb=" CA  LEU H 802 "
        pdb=" C   LEU H 802 "
      ideal   model   delta    sigma   weight residual
     111.36  107.92    3.44 1.09e+00 8.42e-01 9.96e+00
  ... (remaining 18022 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 6504
       35.97 -    71.93: 808
       71.93 -   107.90: 6
      107.90 -   143.86: 1
      143.86 -   179.83: 4
  Dihedral angle restraints: 7323
    sinusoidal: 4182
      harmonic: 3141
  Sorted by residual:
  dihedral pdb=" CA  ILE F 116 "
           pdb=" C   ILE F 116 "
           pdb=" N   PHE F 117 "
           pdb=" CA  PHE F 117 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.28  -22.72     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  VAL H 229 "
           pdb=" C   VAL H 229 "
           pdb=" N   PRO H 230 "
           pdb=" CA  PRO H 230 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.53  -22.47     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  ARG H 807 "
           pdb=" C   ARG H 807 "
           pdb=" N   SER H 808 "
           pdb=" CA  SER H 808 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.17  -19.83     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 7320 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1985
       0.106 -    0.211: 26
       0.211 -    0.317: 0
       0.317 -    0.423: 0
       0.423 -    0.528: 3
  Chirality restraints: 2014
  Sorted by residual:
  chirality pdb=" P    DG A   7 "
            pdb=" OP1  DG A   7 "
            pdb=" OP2  DG A   7 "
            pdb=" O5'  DG A   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.87   -0.53 2.00e-01 2.50e+01 6.97e+00
  chirality pdb=" P    DG A   9 "
            pdb=" OP1  DG A   9 "
            pdb=" OP2  DG A   9 "
            pdb=" O5'  DG A   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.87   -0.52 2.00e-01 2.50e+01 6.88e+00
  chirality pdb=" P    DT A   8 "
            pdb=" OP1  DT A   8 "
            pdb=" OP2  DT A   8 "
            pdb=" O5'  DT A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.82   -0.47 2.00e-01 2.50e+01 5.58e+00
  ... (remaining 2011 not shown)

  Planarity restraints: 1701
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  13 "    0.024 2.00e-02 2.50e+03   1.19e-02 3.56e+00
        pdb=" N1   DT A  13 "   -0.026 2.00e-02 2.50e+03
        pdb=" C2   DT A  13 "   -0.003 2.00e-02 2.50e+03
        pdb=" O2   DT A  13 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DT A  13 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DT A  13 "    0.004 2.00e-02 2.50e+03
        pdb=" O4   DT A  13 "    0.010 2.00e-02 2.50e+03
        pdb=" C5   DT A  13 "    0.000 2.00e-02 2.50e+03
        pdb=" C7   DT A  13 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DT A  13 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA A  81 "   -0.024 2.00e-02 2.50e+03   1.05e-02 3.02e+00
        pdb=" N9   DA A  81 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DA A  81 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA A  81 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DA A  81 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA A  81 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA A  81 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DA A  81 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA A  81 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DA A  81 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DA A  81 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA B  44 "    0.023 2.00e-02 2.50e+03   1.03e-02 2.94e+00
        pdb=" N9   DA B  44 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA B  44 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DA B  44 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DA B  44 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA B  44 "    0.003 2.00e-02 2.50e+03
        pdb=" N6   DA B  44 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA B  44 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2   DA B  44 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA B  44 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA B  44 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1698 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 47
        2.54 -     3.13: 8958
        3.13 -     3.72: 20382
        3.72 -     4.31: 28765
        4.31 -     4.90: 43403
  Nonbonded interactions: 101555
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS H 157 "
            pdb="MG    MG H1801 "
     model   vdw
     1.944 2.250
  nonbonded pdb=" ND1 HIS H 146 "
            pdb="MG    MG H1801 "
     model   vdw
     1.952 2.250
  nonbonded pdb=" OG  SER H   3 "
            pdb=" OG1 THR H  83 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" OP2  DA B  46 "
            pdb=" NH1 ARG C  76 "
     model   vdw
     2.146 3.120
  nonbonded pdb=" NE2 HIS H 159 "
            pdb="MG    MG H1801 "
     model   vdw
     2.184 2.250
  ... (remaining 101550 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'E' and (resid 11 through 16 or (resid 17 through 18 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 19 through 53 or (resid 54 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 55 through 67 or (res \ 
id 68 and (name N or name CA or name C or name O or name CB )) or resid 69 throu \ 
gh 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 78 through 85 or (resid 86 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 87 through 113))
  selection = (chain 'F' and (resid 11 through 16 or (resid 17 through 18 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 19 through 59 or resid 64 through  \ 
67 or (resid 68 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 69 through 85 or (resid 86 and (name N or name CA or name C or name O or name  \ 
CB )) or resid 87 through 113))
  selection = (chain 'G' and (resid 11 through 59 or resid 64 through 76 or (resid 77 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 78 through 113))
}

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 individual isotropic
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:             8.070
  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:             0.010
  Extract box with map and model:          0.530
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     37.410
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
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      :  0.004   0.047  12763  Z= 0.204
  Angle     :  0.600   8.009  18027  Z= 0.360
  Chirality :  0.042   0.528   2014
  Planarity :  0.003   0.030   1701
  Dihedral  : 22.834 179.825   5289
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.69 %
    Favored  : 98.08 %
  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:  0.08 (0.25), residues: 1073
  helix:  0.54 (0.22), residues: 474
  sheet:  0.27 (0.34), residues: 222
  loop : -0.54 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  91 
 HIS   0.004   0.001   HIS H 106 
 PHE   0.012   0.001   PHE H 112 
 TYR   0.011   0.001   TYR H 669 
 ARG   0.003   0.000   ARG G  51 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15243 (  623)
  hydrogen bonds       : angle       5.90545 ( 1618)
  covalent geometry    : bond        0.00434 (12763)
  covalent geometry    : angle       0.59993 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 250
  time to evaluate  : 1.130 
Fit side-chains
   revert: symmetry clash
REVERT: D   81 LYS cc_start: 0.8991 (tttt) cc_final: 0.8662 (tttp)
REVERT: F   12 LYS cc_start: 0.8758 (mttt) cc_final: 0.8522 (mttp)
REVERT: F   46 LYS cc_start: 0.8486 (tttp) cc_final: 0.8174 (ttpp)
REVERT: F   60 ASN cc_start: 0.7346 (t0) cc_final: 0.7027 (t0)
REVERT: F  103 ASP cc_start: 0.8324 (t70) cc_final: 0.8020 (t0)
REVERT: G   43 ILE cc_start: 0.8309 (tp) cc_final: 0.8054 (mt)
REVERT: E    8 SER cc_start: 0.9127 (p) cc_final: 0.8758 (m)
REVERT: E   46 LYS cc_start: 0.9076 (tttt) cc_final: 0.8758 (tttp)
REVERT: H   31 GLU cc_start: 0.7947 (pm20) cc_final: 0.7675 (pm20)
REVERT: H   75 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8409 (mmm-85)
REVERT: H  202 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7377 (pt0)
REVERT: H  573 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7644 (mm-30)
REVERT: H  577 ASN cc_start: 0.8584 (t0) cc_final: 0.8380 (t0)
REVERT: H  656 MET cc_start: 0.9337 (mmm) cc_final: 0.9111 (mtp)
REVERT: H  730 SER cc_start: 0.8573 (t) cc_final: 0.8312 (p)
REVERT: H  797 MET cc_start: 0.8229 (mtp) cc_final: 0.7930 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 252
  average time/residue: 0.3600
  time to fit residues: 116.8265
Evaluate side-chains
  154 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.0670
   chunk 93 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
D  39 GLN
G  79 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.115288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.092241 restraints weight = 21867.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.49
r_work: 0.3047 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12763  Z= 0.169
  Angle     :  0.571   4.690  18027  Z= 0.339
  Chirality :  0.037   0.139   2014
  Planarity :  0.004   0.033   1701
  Dihedral  : 27.267 177.001   3269
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  8.81 %
    Favored  : 89.49 %
  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:  0.60 (0.25), residues: 1073
  helix:  1.30 (0.23), residues: 484
  sheet:  0.11 (0.36), residues: 188
  loop : -0.47 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  91 
 HIS   0.003   0.001   HIS H 159 
 PHE   0.019   0.002   PHE H  16 
 TYR   0.017   0.002   TYR E  52 
 ARG   0.006   0.001   ARG G 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  623)
  hydrogen bonds       : angle       4.16533 ( 1618)
  covalent geometry    : bond        0.00369 (12763)
  covalent geometry    : angle       0.57124 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 1.091 
Fit side-chains
REVERT: C   57 LYS cc_start: 0.9003 (mttt) cc_final: 0.8602 (mttm)
REVERT: F   46 LYS cc_start: 0.8513 (tttp) cc_final: 0.8309 (ttpp)
REVERT: F   60 ASN cc_start: 0.7376 (t0) cc_final: 0.7150 (t0)
REVERT: G   16 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7884 (mp)
REVERT: G   43 ILE cc_start: 0.8497 (tp) cc_final: 0.8209 (mt)
REVERT: E    8 SER cc_start: 0.9031 (p) cc_final: 0.8814 (m)
REVERT: H    1 MET cc_start: 0.8547 (tpt) cc_final: 0.8299 (tpt)
REVERT: H  573 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7422 (mm-30)
  outliers start: 15
  outliers final: 5
  residues processed: 174
  average time/residue: 0.3017
  time to fit residues: 70.6332
Evaluate side-chains
  137 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 131
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   75 LYS
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain H residue  595 GLU
Chi-restraints excluded: chain H residue  697 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 122 optimal weight:    0.2980
   chunk 55 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0870
   chunk 73 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
F 104 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.115104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.091546 restraints weight = 22149.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.49
r_work: 0.3042 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2914 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
moved from start:          0.2397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12763  Z= 0.168
  Angle     :  0.562   5.824  18027  Z= 0.330
  Chirality :  0.036   0.139   2014
  Planarity :  0.004   0.036   1701
  Dihedral  : 27.252 178.253   3269
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  9.83 %
    Favored  : 88.25 %
  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:  0.77 (0.26), residues: 1073
  helix:  1.46 (0.23), residues: 483
  sheet:  0.24 (0.34), residues: 217
  loop : -0.49 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  91 
 HIS   0.003   0.001   HIS H 159 
 PHE   0.011   0.001   PHE H  16 
 TYR   0.014   0.002   TYR D  55 
 ARG   0.006   0.001   ARG H  75 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  623)
  hydrogen bonds       : angle       3.93078 ( 1618)
  covalent geometry    : bond        0.00371 (12763)
  covalent geometry    : angle       0.56231 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 149
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
REVERT: F   46 LYS cc_start: 0.8569 (tttp) cc_final: 0.8339 (ttpp)
REVERT: F   60 ASN cc_start: 0.7491 (t0) cc_final: 0.7205 (t0)
REVERT: H  166 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8421 (t)
REVERT: H  573 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7354 (mm-30)
REVERT: H  577 ASN cc_start: 0.8345 (t0) cc_final: 0.8100 (t0)
  outliers start: 17
  outliers final: 9
  residues processed: 161
  average time/residue: 0.2966
  time to fit residues: 65.5889
Evaluate side-chains
  137 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 127
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue  166 THR
Chi-restraints excluded: chain H residue  595 GLU
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  697 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 98 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 108 optimal weight:    0.5980
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
H 108 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.113013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.089457 restraints weight = 21932.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.45
r_work: 0.3009 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12763  Z= 0.202
  Angle     :  0.583   8.259  18027  Z= 0.339
  Chirality :  0.037   0.142   2014
  Planarity :  0.004   0.045   1701
  Dihedral  : 27.388 176.496   3269
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 11.53 %
    Favored  : 85.88 %
  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:  0.60 (0.25), residues: 1073
  helix:  1.37 (0.23), residues: 482
  sheet:  0.08 (0.33), residues: 218
  loop : -0.58 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  91 
 HIS   0.004   0.001   HIS H 159 
 PHE   0.010   0.002   PHE G  39 
 TYR   0.013   0.002   TYR H 669 
 ARG   0.007   0.001   ARG G 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04322 (  623)
  hydrogen bonds       : angle       4.01065 ( 1618)
  covalent geometry    : bond        0.00454 (12763)
  covalent geometry    : angle       0.58265 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 147
  time to evaluate  : 1.209 
Fit side-chains
REVERT: C   28 GLU cc_start: 0.8730 (tp30) cc_final: 0.8468 (tp30)
REVERT: F   46 LYS cc_start: 0.8577 (tttp) cc_final: 0.8325 (ttpp)
REVERT: F   60 ASN cc_start: 0.7628 (t0) cc_final: 0.7316 (t0)
REVERT: E  107 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8704 (mttp)
REVERT: H    1 MET cc_start: 0.8571 (tpt) cc_final: 0.8263 (tpt)
REVERT: H  573 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7289 (mm-30)
REVERT: H  577 ASN cc_start: 0.8329 (t0) cc_final: 0.8071 (t0)
  outliers start: 23
  outliers final: 12
  residues processed: 164
  average time/residue: 0.3114
  time to fit residues: 69.2064
Evaluate side-chains
  145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue  127 THR
Chi-restraints excluded: chain H residue  595 GLU
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  697 SER
Chi-restraints excluded: chain H residue  729 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 119 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 114 optimal weight:    0.8980
   chunk 98 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0870
   chunk 51 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.113956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.090226 restraints weight = 22073.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.41
r_work: 0.3028 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12763  Z= 0.167
  Angle     :  0.557   6.595  18027  Z= 0.327
  Chirality :  0.036   0.146   2014
  Planarity :  0.004   0.038   1701
  Dihedral  : 27.252 176.626   3269
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.88 %
    Favored  : 84.97 %
  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:  0.64 (0.25), residues: 1073
  helix:  1.49 (0.23), residues: 482
  sheet: -0.04 (0.33), residues: 218
  loop : -0.61 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  91 
 HIS   0.003   0.001   HIS H 159 
 PHE   0.010   0.001   PHE H 112 
 TYR   0.018   0.002   TYR G  52 
 ARG   0.006   0.000   ARG C  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03855 (  623)
  hydrogen bonds       : angle       3.89840 ( 1618)
  covalent geometry    : bond        0.00371 (12763)
  covalent geometry    : angle       0.55693 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 1.233 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8567 (tttp) cc_final: 0.8308 (ttpp)
REVERT: F   60 ASN cc_start: 0.7610 (t0) cc_final: 0.7275 (t0)
REVERT: H  573 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7264 (mm-30)
REVERT: H  577 ASN cc_start: 0.8341 (t0) cc_final: 0.8084 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 163
  average time/residue: 0.3204
  time to fit residues: 69.8471
Evaluate side-chains
  149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue  127 THR
Chi-restraints excluded: chain H residue  202 GLU
Chi-restraints excluded: chain H residue  595 GLU
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  697 SER
Chi-restraints excluded: chain H residue  729 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 63 optimal weight:    0.3980
   chunk 122 optimal weight:    0.0470
   chunk 31 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 41 optimal weight:    0.1980
   chunk 106 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 85 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 117 optimal weight:    0.5980
   chunk 92 optimal weight:    0.0270
   overall best weight:    0.2536

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.117427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.094485 restraints weight = 22319.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 1.42
r_work: 0.3098 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12763  Z= 0.134
  Angle     :  0.539   6.697  18027  Z= 0.317
  Chirality :  0.035   0.152   2014
  Planarity :  0.003   0.039   1701
  Dihedral  : 26.999 175.786   3269
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.11 %
    Favored  : 84.86 %
  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:  0.86 (0.26), residues: 1073
  helix:  1.73 (0.23), residues: 482
  sheet:  0.15 (0.33), residues: 218
  loop : -0.64 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F  91 
 HIS   0.003   0.001   HIS H 159 
 PHE   0.011   0.001   PHE H 112 
 TYR   0.015   0.001   TYR G  52 
 ARG   0.008   0.000   ARG C  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03335 (  623)
  hydrogen bonds       : angle       3.73526 ( 1618)
  covalent geometry    : bond        0.00287 (12763)
  covalent geometry    : angle       0.53873 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 1.347 
Fit side-chains
REVERT: D   17 ILE cc_start: 0.9353 (mt) cc_final: 0.9120 (tt)
REVERT: F   46 LYS cc_start: 0.8504 (tttp) cc_final: 0.8244 (ttpp)
REVERT: G   16 LEU cc_start: 0.8272 (mp) cc_final: 0.8056 (mt)
REVERT: E  112 TYR cc_start: 0.7704 (m-80) cc_final: 0.7489 (m-80)
REVERT: H  573 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7245 (mm-30)
REVERT: H  577 ASN cc_start: 0.8291 (t0) cc_final: 0.8020 (t0)
  outliers start: 18
  outliers final: 13
  residues processed: 161
  average time/residue: 0.2627
  time to fit residues: 59.0762
Evaluate side-chains
  146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   92 MET
Chi-restraints excluded: chain H residue   95 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  697 SER
Chi-restraints excluded: chain H residue  729 VAL
Chi-restraints excluded: chain H residue  782 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 117 optimal weight:    0.2980
   chunk 41 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 106 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 121 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.114460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.090807 restraints weight = 22173.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 1.46
r_work: 0.3028 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12763  Z= 0.181
  Angle     :  0.568   7.664  18027  Z= 0.330
  Chirality :  0.036   0.163   2014
  Planarity :  0.004   0.039   1701
  Dihedral  : 27.190 173.690   3269
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.58 %
    Favored  : 83.39 %
  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:  0.83 (0.26), residues: 1073
  helix:  1.73 (0.24), residues: 481
  sheet:  0.06 (0.32), residues: 221
  loop : -0.64 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP G  91 
 HIS   0.004   0.001   HIS H 159 
 PHE   0.009   0.001   PHE H 112 
 TYR   0.014   0.002   TYR G  52 
 ARG   0.009   0.000   ARG E  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (  623)
  hydrogen bonds       : angle       3.80529 ( 1618)
  covalent geometry    : bond        0.00404 (12763)
  covalent geometry    : angle       0.56791 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 1.069 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8624 (tttp) cc_final: 0.8366 (ttpp)
REVERT: F   60 ASN cc_start: 0.7475 (t0) cc_final: 0.7065 (t0)
REVERT: E    1 MET cc_start: 0.7373 (mtm) cc_final: 0.7090 (ttm)
REVERT: H  573 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7295 (mm-30)
REVERT: H  577 ASN cc_start: 0.8339 (t0) cc_final: 0.8071 (t0)
  outliers start: 18
  outliers final: 18
  residues processed: 147
  average time/residue: 0.2536
  time to fit residues: 53.0900
Evaluate side-chains
  148 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   92 MET
Chi-restraints excluded: chain H residue   93 MET
Chi-restraints excluded: chain H residue   95 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  697 SER
Chi-restraints excluded: chain H residue  729 VAL
Chi-restraints excluded: chain H residue  782 VAL
Chi-restraints excluded: chain H residue  823 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:    0.0670
   chunk 79 optimal weight:    4.9990
   chunk 112 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 122 optimal weight:   10.0000
   chunk 86 optimal weight:    0.8980
   chunk 98 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   overall best weight:    0.9120

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.112553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.088657 restraints weight = 22361.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.41
r_work: 0.3001 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12763  Z= 0.204
  Angle     :  0.586   8.188  18027  Z= 0.340
  Chirality :  0.037   0.158   2014
  Planarity :  0.004   0.039   1701
  Dihedral  : 27.350 172.164   3269
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.80 %
    Favored  : 83.39 %
  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:  0.71 (0.26), residues: 1073
  helix:  1.68 (0.23), residues: 481
  sheet: -0.11 (0.32), residues: 223
  loop : -0.68 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  91 
 HIS   0.005   0.001   HIS H 157 
 PHE   0.010   0.002   PHE F 111 
 TYR   0.013   0.002   TYR G  52 
 ARG   0.008   0.000   ARG C  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  623)
  hydrogen bonds       : angle       3.89455 ( 1618)
  covalent geometry    : bond        0.00459 (12763)
  covalent geometry    : angle       0.58644 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 138
  time to evaluate  : 1.060 
Fit side-chains
REVERT: C   10 GLU cc_start: 0.8262 (tt0) cc_final: 0.8052 (mt-10)
REVERT: F   46 LYS cc_start: 0.8659 (tttp) cc_final: 0.8418 (ttpp)
REVERT: F   60 ASN cc_start: 0.7543 (t0) cc_final: 0.7223 (t0)
REVERT: E    1 MET cc_start: 0.7356 (mtm) cc_final: 0.7054 (ttm)
REVERT: H  100 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7976 (mmtt)
REVERT: H  573 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7244 (mm-30)
REVERT: H  577 ASN cc_start: 0.8357 (t0) cc_final: 0.8111 (t0)
REVERT: H  797 MET cc_start: 0.8157 (mtp) cc_final: 0.7892 (mtt)
  outliers start: 16
  outliers final: 15
  residues processed: 149
  average time/residue: 0.2621
  time to fit residues: 55.0490
Evaluate side-chains
  146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   95 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  697 SER
Chi-restraints excluded: chain H residue  729 VAL
Chi-restraints excluded: chain H residue  782 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0870
   chunk 9 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 94 optimal weight:    0.2980
   chunk 122 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.5758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.114286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.090997 restraints weight = 22151.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.37
r_work: 0.3045 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12763  Z= 0.163
  Angle     :  0.571   9.747  18027  Z= 0.331
  Chirality :  0.036   0.162   2014
  Planarity :  0.004   0.039   1701
  Dihedral  : 27.238 172.541   3269
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.48 %
    Favored  : 82.49 %
  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:  0.72 (0.25), residues: 1073
  helix:  1.69 (0.23), residues: 481
  sheet: -0.12 (0.32), residues: 223
  loop : -0.70 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP G  91 
 HIS   0.004   0.001   HIS H 157 
 PHE   0.009   0.001   PHE H 112 
 TYR   0.022   0.001   TYR G  52 
 ARG   0.009   0.000   ARG C  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  623)
  hydrogen bonds       : angle       3.82262 ( 1618)
  covalent geometry    : bond        0.00362 (12763)
  covalent geometry    : angle       0.57055 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 1.073 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8644 (tttp) cc_final: 0.8389 (ttpp)
REVERT: F   60 ASN cc_start: 0.7469 (t0) cc_final: 0.7161 (t0)
REVERT: G   72 MET cc_start: 0.7784 (mtp) cc_final: 0.7475 (ptp)
REVERT: G   91 TRP cc_start: 0.5957 (m-90) cc_final: 0.5612 (m100)
REVERT: E    1 MET cc_start: 0.7337 (mtm) cc_final: 0.7061 (ttm)
REVERT: H   29 MET cc_start: 0.6726 (tpp) cc_final: 0.6387 (mmm)
REVERT: H   56 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8835 (mp)
REVERT: H  100 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7917 (mmtt)
REVERT: H  573 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7203 (mm-30)
REVERT: H  577 ASN cc_start: 0.8320 (t0) cc_final: 0.8068 (t0)
REVERT: H  797 MET cc_start: 0.8038 (mtp) cc_final: 0.7818 (mtt)
  outliers start: 18
  outliers final: 15
  residues processed: 148
  average time/residue: 0.2519
  time to fit residues: 52.9893
Evaluate side-chains
  144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain H residue   56 LEU
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   95 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  697 SER
Chi-restraints excluded: chain H residue  729 VAL
Chi-restraints excluded: chain H residue  782 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 117 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 110 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.112942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.089221 restraints weight = 22118.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 1.46
r_work: 0.3010 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.3407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12763  Z= 0.195
  Angle     :  0.584  10.231  18027  Z= 0.339
  Chirality :  0.037   0.164   2014
  Planarity :  0.004   0.039   1701
  Dihedral  : 27.338 170.877   3269
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.48 %
    Favored  : 82.71 %
  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:  0.63 (0.26), residues: 1073
  helix:  1.61 (0.24), residues: 481
  sheet: -0.19 (0.33), residues: 223
  loop : -0.70 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP G  91 
 HIS   0.005   0.001   HIS H 157 
 PHE   0.009   0.002   PHE H 112 
 TYR   0.020   0.002   TYR G  52 
 ARG   0.009   0.000   ARG C  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  623)
  hydrogen bonds       : angle       3.90954 ( 1618)
  covalent geometry    : bond        0.00439 (12763)
  covalent geometry    : angle       0.58445 (18027)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 1.056 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8638 (tttp) cc_final: 0.8387 (ttpp)
REVERT: F   60 ASN cc_start: 0.7540 (t0) cc_final: 0.7220 (t0)
REVERT: G   91 TRP cc_start: 0.6137 (m-90) cc_final: 0.5682 (m100)
REVERT: E    1 MET cc_start: 0.7362 (mtm) cc_final: 0.7060 (ttm)
REVERT: H   29 MET cc_start: 0.6771 (tpp) cc_final: 0.6438 (mmm)
REVERT: H   56 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8896 (mp)
REVERT: H  100 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7877 (mmtt)
REVERT: H  573 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7241 (mm-30)
REVERT: H  577 ASN cc_start: 0.8349 (t0) cc_final: 0.8099 (t0)
REVERT: H  797 MET cc_start: 0.8095 (mtp) cc_final: 0.7860 (mtt)
  outliers start: 16
  outliers final: 15
  residues processed: 147
  average time/residue: 0.2624
  time to fit residues: 54.3923
Evaluate side-chains
  148 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   60 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain F residue   33 SER
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain E residue   33 SER
Chi-restraints excluded: chain H residue   56 LEU
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   95 MET
Chi-restraints excluded: chain H residue  693 VAL
Chi-restraints excluded: chain H residue  697 SER
Chi-restraints excluded: chain H residue  729 VAL
Chi-restraints excluded: chain H residue  782 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0770
   chunk 88 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0470
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.4636

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.115349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.092575 restraints weight = 22105.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.45
r_work: 0.3051 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.3541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12763  Z= 0.151
  Angle     :  0.558  10.105  18027  Z= 0.325
  Chirality :  0.035   0.153   2014
  Planarity :  0.004   0.038   1701
  Dihedral  : 27.150 171.634   3269
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.59 %
    Favored  : 82.37 %
  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:  0.72 (0.26), residues: 1073
  helix:  1.68 (0.24), residues: 481
  sheet: -0.11 (0.33), residues: 223
  loop : -0.69 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G  91 
 HIS   0.004   0.001   HIS H 157 
 PHE   0.009   0.001   PHE H 112 
 TYR   0.018   0.001   TYR E  52 
 ARG   0.009   0.000   ARG C  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03540 (  623)
  hydrogen bonds       : angle       3.78717 ( 1618)
  covalent geometry    : bond        0.00333 (12763)
  covalent geometry    : angle       0.55799 (18027)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8280.90 seconds
wall clock time: 144 minutes 6.04 seconds (8646.04 seconds total)