Starting phenix.real_space_refine
on Sat Aug 23 12:16:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f12_50122/08_2025/9f12_50122.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f12_50122/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f12_50122/08_2025/9f12_50122.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f12_50122/08_2025/9f12_50122.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f12_50122/08_2025/9f12_50122.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f12_50122/08_2025/9f12_50122.map"
  }
  resolution = 3.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 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: {'ARG:plan': 6, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 1}
          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: 2.77, per 1000 atoms: 0.23
  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: 0.76
  Conformation dependent library (CDL) restraints added in 399.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 1.73
  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: 2.75

  Time building geometry restraints manager: 1.02 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:             12.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.840
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.670
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG G  51 
 TYR   0.011   0.001   TYR H 669 
 PHE   0.012   0.001   PHE H 112 
 TRP   0.010   0.001   TRP F  91 
 HIS   0.004   0.001   HIS H 106 

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

*********************** 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  : 0.376 
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: 0.7957 (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: 0.1579
  time to fit residues: 51.3830
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  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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
G 104 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.114000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.090676 restraints weight = 21983.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.55
r_work: 0.3007 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.1933

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= 0.192
  Angle     :  0.586   4.841  18027  Z= 0.346
  Chirality :  0.038   0.144   2014
  Planarity :  0.004   0.033   1701
  Dihedral  : 27.359 177.053   3269
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  8.93 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.25), residues: 1073
  helix:  1.24 (0.23), residues: 484
  sheet:  0.04 (0.36), residues: 188
  loop : -0.50 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  54 
 TYR   0.017   0.002   TYR E  52 
 PHE   0.020   0.002   PHE H  16 
 TRP   0.009   0.001   TRP F  91 
 HIS   0.003   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (12763)
  covalent geometry    : angle       0.58558 (18027)
  hydrogen bonds       : bond        0.04600 (  623)
  hydrogen bonds       : angle       4.20360 ( 1618)

*********************** 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
  177 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.412 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8532 (tttp) cc_final: 0.8326 (ttpp)
REVERT: G   16 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.7972 (mp)
REVERT: G   43 ILE cc_start: 0.8548 (tp) cc_final: 0.8226 (mt)
REVERT: E    8 SER cc_start: 0.9095 (p) cc_final: 0.8810 (m)
REVERT: H  573 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7442 (mm-30)
  outliers start: 18
  outliers final: 7
  residues processed: 172
  average time/residue: 0.1441
  time to fit residues: 33.5971
Evaluate side-chains
  137 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   47 SER
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 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 63 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 64 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
F 104 HIS
H 108 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.109868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.085684 restraints weight = 22308.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.48
r_work: 0.2946 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2820 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045  12763  Z= 0.295
  Angle     :  0.656   6.503  18027  Z= 0.379
  Chirality :  0.042   0.143   2014
  Planarity :  0.005   0.042   1701
  Dihedral  : 27.852 177.730   3269
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 10.17 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.25), residues: 1073
  helix:  1.01 (0.23), residues: 485
  sheet: -0.13 (0.35), residues: 206
  loop : -0.68 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  51 
 TYR   0.021   0.002   TYR F  52 
 PHE   0.013   0.002   PHE E  55 
 TRP   0.008   0.001   TRP H  33 
 HIS   0.005   0.001   HIS H 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 (12763)
  covalent geometry    : angle       0.65560 (18027)
  hydrogen bonds       : bond        0.05455 (  623)
  hydrogen bonds       : angle       4.30956 ( 1618)

*********************** 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
  178 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 155
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 GLU cc_start: 0.8794 (tp30) cc_final: 0.8564 (tp30)
REVERT: F   46 LYS cc_start: 0.8656 (tttp) cc_final: 0.8407 (ttpp)
REVERT: H    1 MET cc_start: 0.8659 (tpt) cc_final: 0.8449 (tpt)
REVERT: H  573 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7296 (mm-30)
REVERT: H  577 ASN cc_start: 0.8335 (t0) cc_final: 0.8134 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 173
  average time/residue: 0.1331
  time to fit residues: 31.3806
Evaluate side-chains
  149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
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 F residue   71 THR
Chi-restraints excluded: chain G residue   46 LYS
Chi-restraints excluded: chain G residue  106 ILE
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  141 MET
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 116 optimal weight:    0.0570
   chunk 52 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 119 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 117 optimal weight:    0.0060
   chunk 111 optimal weight:    0.7980
   chunk 89 optimal weight:    0.5980
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.3314

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.114855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.091289 restraints weight = 22043.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.41
r_work: 0.3048 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12763  Z= 0.144
  Angle     :  0.552   6.775  18027  Z= 0.327
  Chirality :  0.036   0.141   2014
  Planarity :  0.004   0.038   1701
  Dihedral  : 27.294 178.289   3269
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.85 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.25), residues: 1073
  helix:  1.40 (0.23), residues: 480
  sheet: -0.04 (0.33), residues: 215
  loop : -0.65 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G 100 
 TYR   0.012   0.001   TYR D  55 
 PHE   0.017   0.001   PHE G 108 
 TRP   0.008   0.001   TRP G  91 
 HIS   0.004   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (12763)
  covalent geometry    : angle       0.55216 (18027)
  hydrogen bonds       : bond        0.03730 (  623)
  hydrogen bonds       : angle       3.93000 ( 1618)

*********************** 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
  169 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.288 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8518 (tttp) cc_final: 0.8280 (ttpp)
REVERT: H  573 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7223 (mm-30)
REVERT: H  577 ASN cc_start: 0.8334 (t0) cc_final: 0.8103 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 163
  average time/residue: 0.1410
  time to fit residues: 30.9685
Evaluate side-chains
  143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
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   25 LEU
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain H residue   91 SER
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  823 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 102 optimal weight:    0.3980
   chunk 52 optimal weight:    0.0770
   chunk 28 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 79 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.5740

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

Flipped N/Q/H residues before XYZ refinement:
F  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.114006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.090224 restraints weight = 22237.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.44
r_work: 0.3028 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.3025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12763  Z= 0.164
  Angle     :  0.560   7.143  18027  Z= 0.327
  Chirality :  0.036   0.144   2014
  Planarity :  0.004   0.038   1701
  Dihedral  : 27.334 176.173   3269
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.19 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.26), residues: 1073
  helix:  1.50 (0.23), residues: 483
  sheet: -0.04 (0.33), residues: 218
  loop : -0.64 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  82 
 TYR   0.016   0.001   TYR E  52 
 PHE   0.010   0.001   PHE H 112 
 TRP   0.010   0.001   TRP F  91 
 HIS   0.004   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12763)
  covalent geometry    : angle       0.56036 (18027)
  hydrogen bonds       : bond        0.03865 (  623)
  hydrogen bonds       : angle       3.88057 ( 1618)

*********************** 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
  163 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 141
  time to evaluate  : 0.406 
Fit side-chains
REVERT: C   10 GLU cc_start: 0.8226 (tt0) cc_final: 0.8017 (mt-10)
REVERT: F   46 LYS cc_start: 0.8576 (tttp) cc_final: 0.8335 (ttpp)
REVERT: F  102 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8545 (mp)
REVERT: G   16 LEU cc_start: 0.8504 (mp) cc_final: 0.8238 (mt)
REVERT: H  573 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7218 (mm-30)
REVERT: H  577 ASN cc_start: 0.8366 (t0) cc_final: 0.8121 (t0)
REVERT: H  595 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6882 (tm-30)
  outliers start: 22
  outliers final: 13
  residues processed: 155
  average time/residue: 0.1351
  time to fit residues: 28.7071
Evaluate side-chains
  147 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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 F residue  102 ILE
Chi-restraints excluded: chain G residue   25 LEU
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
Chi-restraints excluded: chain H residue  823 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 59 optimal weight:    0.3980
   chunk 85 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8786

-------------------------------------------------------------------------------
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 = 0.112508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.088759 restraints weight = 22120.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.42
r_work: 0.3002 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12763  Z= 0.199
  Angle     :  0.574   7.163  18027  Z= 0.335
  Chirality :  0.037   0.152   2014
  Planarity :  0.004   0.039   1701
  Dihedral  : 27.406 174.814   3269
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 12.54 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.26), residues: 1073
  helix:  1.52 (0.24), residues: 480
  sheet: -0.16 (0.34), residues: 208
  loop : -0.66 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  82 
 TYR   0.014   0.002   TYR E  52 
 PHE   0.017   0.002   PHE G 108 
 TRP   0.007   0.001   TRP F  91 
 HIS   0.004   0.001   HIS H 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (12763)
  covalent geometry    : angle       0.57441 (18027)
  hydrogen bonds       : bond        0.04200 (  623)
  hydrogen bonds       : angle       3.94005 ( 1618)

*********************** 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
  153 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.283 
Fit side-chains
REVERT: C   10 GLU cc_start: 0.8262 (tt0) cc_final: 0.8047 (mt-10)
REVERT: F   46 LYS cc_start: 0.8574 (tttp) cc_final: 0.8348 (ttpp)
REVERT: F  102 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8611 (mp)
REVERT: H   56 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8896 (mp)
REVERT: H  573 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7230 (mm-30)
REVERT: H  577 ASN cc_start: 0.8384 (t0) cc_final: 0.8140 (t0)
REVERT: H  595 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6939 (tm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 147
  average time/residue: 0.1177
  time to fit residues: 24.2572
Evaluate side-chains
  142 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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 F residue   43 ILE
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain E residue    6 THR
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  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
Chi-restraints excluded: chain H residue  782 VAL
Chi-restraints excluded: chain H residue  823 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0020
   chunk 74 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.114581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.091440 restraints weight = 22079.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.40
r_work: 0.3052 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.3257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12763  Z= 0.156
  Angle     :  0.553   7.703  18027  Z= 0.323
  Chirality :  0.035   0.158   2014
  Planarity :  0.004   0.038   1701
  Dihedral  : 27.246 174.536   3269
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 12.54 %
    Favored  : 85.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.26), residues: 1073
  helix:  1.61 (0.24), residues: 480
  sheet: -0.08 (0.33), residues: 218
  loop : -0.65 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  82 
 TYR   0.013   0.001   TYR E  52 
 PHE   0.018   0.001   PHE G 108 
 TRP   0.007   0.001   TRP F  91 
 HIS   0.003   0.001   HIS H 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12763)
  covalent geometry    : angle       0.55340 (18027)
  hydrogen bonds       : bond        0.03704 (  623)
  hydrogen bonds       : angle       3.82834 ( 1618)

*********************** 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
  155 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.371 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8564 (tttp) cc_final: 0.8314 (ttpp)
REVERT: F  102 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8561 (mp)
REVERT: E    1 MET cc_start: 0.7251 (mtm) cc_final: 0.7001 (ttm)
REVERT: H   56 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8838 (mp)
REVERT: H  573 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7181 (mm-30)
REVERT: H  577 ASN cc_start: 0.8334 (t0) cc_final: 0.8084 (t0)
REVERT: H  595 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6833 (tm-30)
  outliers start: 21
  outliers final: 15
  residues processed: 147
  average time/residue: 0.1204
  time to fit residues: 24.4322
Evaluate side-chains
  145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
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 F residue  102 ILE
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain H residue   56 LEU
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   93 MET
Chi-restraints excluded: chain H residue   95 MET
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
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 52 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 119 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3527 r_free = 0.3527 target = 0.112348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.088535 restraints weight = 22195.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 1.44
r_work: 0.2999 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  12763  Z= 0.210
  Angle     :  0.581   9.240  18027  Z= 0.339
  Chirality :  0.037   0.162   2014
  Planarity :  0.004   0.039   1701
  Dihedral  : 27.444 172.192   3269
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.11 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.26), residues: 1073
  helix:  1.54 (0.23), residues: 480
  sheet: -0.25 (0.34), residues: 208
  loop : -0.67 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  82 
 TYR   0.014   0.002   TYR F  52 
 PHE   0.011   0.002   PHE H 112 
 TRP   0.024   0.001   TRP G  91 
 HIS   0.005   0.001   HIS H 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (12763)
  covalent geometry    : angle       0.58109 (18027)
  hydrogen bonds       : bond        0.04291 (  623)
  hydrogen bonds       : angle       3.94432 ( 1618)

*********************** 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
  149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.409 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8584 (tttp) cc_final: 0.8358 (ttpp)
REVERT: F   60 ASN cc_start: 0.7188 (t0) cc_final: 0.6952 (t0)
REVERT: F  102 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8611 (mp)
REVERT: E    1 MET cc_start: 0.7294 (mtm) cc_final: 0.7041 (ttm)
REVERT: H   29 MET cc_start: 0.6688 (tpp) cc_final: 0.6255 (mmm)
REVERT: H   56 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8926 (mp)
REVERT: H  573 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7208 (mm-30)
REVERT: H  577 ASN cc_start: 0.8364 (t0) cc_final: 0.8120 (t0)
REVERT: H  595 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6961 (tm-30)
  outliers start: 22
  outliers final: 16
  residues processed: 142
  average time/residue: 0.1159
  time to fit residues: 23.3779
Evaluate side-chains
  145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
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 F residue  102 ILE
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain H residue   56 LEU
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   93 MET
Chi-restraints excluded: chain H residue   95 MET
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
Chi-restraints excluded: chain H residue  782 VAL
Chi-restraints excluded: chain H residue  823 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 106 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0970
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3551 r_free = 0.3551 target = 0.113955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.090544 restraints weight = 22120.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.44
r_work: 0.3032 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2905 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8633
moved from start:          0.3373

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= 0.165
  Angle     :  0.563  10.145  18027  Z= 0.329
  Chirality :  0.036   0.163   2014
  Planarity :  0.004   0.038   1701
  Dihedral  : 27.312 172.469   3269
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 13.79 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.25), residues: 1073
  helix:  1.65 (0.24), residues: 478
  sheet: -0.25 (0.34), residues: 208
  loop : -0.69 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  82 
 TYR   0.012   0.001   TYR E  52 
 PHE   0.016   0.001   PHE G  55 
 TRP   0.009   0.001   TRP G  91 
 HIS   0.004   0.001   HIS H 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12763)
  covalent geometry    : angle       0.56346 (18027)
  hydrogen bonds       : bond        0.03834 (  623)
  hydrogen bonds       : angle       3.85505 ( 1618)

*********************** 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
  150 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.285 
Fit side-chains
REVERT: F   46 LYS cc_start: 0.8557 (tttp) cc_final: 0.8328 (ttpp)
REVERT: F   60 ASN cc_start: 0.7169 (t0) cc_final: 0.6942 (t0)
REVERT: F  102 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8582 (mp)
REVERT: E    1 MET cc_start: 0.7341 (mtm) cc_final: 0.7113 (ttm)
REVERT: H   29 MET cc_start: 0.6651 (tpp) cc_final: 0.6263 (mmm)
REVERT: H   56 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8870 (mp)
REVERT: H  573 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7196 (mm-30)
REVERT: H  577 ASN cc_start: 0.8335 (t0) cc_final: 0.8095 (t0)
REVERT: H  595 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6902 (tm-30)
  outliers start: 20
  outliers final: 14
  residues processed: 144
  average time/residue: 0.1170
  time to fit residues: 23.3883
Evaluate side-chains
  143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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 F residue   33 SER
Chi-restraints excluded: chain F residue  102 ILE
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain H residue   56 LEU
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   93 MET
Chi-restraints excluded: chain H residue   95 MET
Chi-restraints excluded: chain H residue  141 MET
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
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 19 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 59 optimal weight:    0.3980
   chunk 54 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 27 optimal weight:    0.1980
   chunk 68 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3562 r_free = 0.3562 target = 0.114672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.091368 restraints weight = 22124.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.43
r_work: 0.3049 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.3473

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= 0.161
  Angle     :  0.564  10.655  18027  Z= 0.328
  Chirality :  0.035   0.159   2014
  Planarity :  0.004   0.038   1701
  Dihedral  : 27.275 171.625   3269
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.46 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.25), residues: 1073
  helix:  1.70 (0.24), residues: 478
  sheet: -0.22 (0.34), residues: 208
  loop : -0.72 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  82 
 TYR   0.012   0.001   TYR E  52 
 PHE   0.011   0.001   PHE H 112 
 TRP   0.007   0.001   TRP F  91 
 HIS   0.004   0.001   HIS H 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (12763)
  covalent geometry    : angle       0.56361 (18027)
  hydrogen bonds       : bond        0.03750 (  623)
  hydrogen bonds       : angle       3.81677 ( 1618)

********************** 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
  154 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: F   46 LYS cc_start: 0.8544 (tttp) cc_final: 0.8327 (ttpp)
REVERT: F   60 ASN cc_start: 0.7210 (t0) cc_final: 0.6983 (t0)
REVERT: G   72 MET cc_start: 0.7729 (mtp) cc_final: 0.7289 (ptp)
REVERT: E    1 MET cc_start: 0.7360 (mtm) cc_final: 0.7138 (ttm)
REVERT: H   29 MET cc_start: 0.6689 (tpp) cc_final: 0.6301 (mmm)
REVERT: H   56 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8851 (mp)
REVERT: H  573 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7210 (mm-30)
REVERT: H  577 ASN cc_start: 0.8316 (t0) cc_final: 0.8069 (t0)
REVERT: H  595 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6844 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 147
  average time/residue: 0.1247
  time to fit residues: 25.3574
Evaluate side-chains
  146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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 F residue   33 SER
Chi-restraints excluded: chain G residue   25 LEU
Chi-restraints excluded: chain E residue    6 THR
Chi-restraints excluded: chain H residue   56 LEU
Chi-restraints excluded: chain H residue   91 SER
Chi-restraints excluded: chain H residue   93 MET
Chi-restraints excluded: chain H residue   95 MET
Chi-restraints excluded: chain H residue  141 MET
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
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 80 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 117 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   chunk 19 optimal weight:    0.3980
   chunk 121 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.113636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.090185 restraints weight = 22165.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.44
r_work: 0.3023 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8647
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12763  Z= 0.185
  Angle     :  0.580  10.757  18027  Z= 0.336
  Chirality :  0.037   0.159   2014
  Planarity :  0.004   0.039   1701
  Dihedral  : 27.332 170.392   3269
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 14.80 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.25), residues: 1073
  helix:  1.63 (0.23), residues: 479
  sheet: -0.27 (0.34), residues: 208
  loop : -0.75 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  82 
 TYR   0.012   0.001   TYR F  52 
 PHE   0.011   0.001   PHE H 112 
 TRP   0.007   0.001   TRP F  91 
 HIS   0.005   0.001   HIS H 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (12763)
  covalent geometry    : angle       0.57969 (18027)
  hydrogen bonds       : bond        0.03997 (  623)
  hydrogen bonds       : angle       3.87003 ( 1618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3236.75 seconds
wall clock time: 56 minutes 3.68 seconds (3363.68 seconds total)