Starting phenix.real_space_refine
on Sun Apr  5 05:26:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw1_54295/04_2026/9rw1_54295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw1_54295/04_2026/9rw1_54295.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw1_54295/04_2026/9rw1_54295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw1_54295/04_2026/9rw1_54295.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw1_54295/04_2026/9rw1_54295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw1_54295/04_2026/9rw1_54295.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      88      5.49       5
     S      24      5.16       5
     C    4841      2.51       5
     N    1526      2.21       5
     O    1887      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8366
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 412
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 412
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "D"
      Number of atoms: 2925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 2925
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          Chain breaks: 3
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 833
          Unresolved non-hydrogen angles: 1060
          Unresolved non-hydrogen dihedrals: 678
          Unresolved non-hydrogen chiralities: 82
          Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 16, 'TYR:plan': 9, 'ASP:plan': 14, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 11, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 438
    Chain: "C"
      Number of atoms: 2767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 2767
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 274}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448}
          Chain breaks: 3
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 981
          Unresolved non-hydrogen angles: 1242
          Unresolved non-hydrogen dihedrals: 801
          Unresolved non-hydrogen chiralities: 94
          Planarities with less than four sites: {'GLU:plan': 22, 'ASN:plan1': 17, 'TYR:plan': 12, 'ASP:plan': 16, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 15, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 512
    Chain: "E"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
    Chain: "F"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
  Time building chain proxies: 2.07, per 1000 atoms: 0.25
  Number of scatterers: 8366
  At special positions: 0
  Unit cell: (87.897, 91.074, 182.148, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      88     15.00
     O    1887      8.00
     N    1526      7.00
     C    4841      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 296.1 milliseconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 6 sheets defined
      69.1% alpha, 6.4% beta
      35 base pairs and 53 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.598A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 747
    Processing helix  chain 'D' and resid 3 through 25
      removed outlier: 3.733A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 36
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 43 through 50
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 110
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.939A  pdb=" N   HIS D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 129
    Processing helix  chain 'D' and resid 130 through 138
    Processing helix  chain 'D' and resid 140 through 151
    Processing helix  chain 'D' and resid 521 through 529
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 3.811A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
    Processing helix  chain 'D' and resid 618 through 629
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 654 through 658
    Processing helix  chain 'D' and resid 662 through 670
      removed outlier: 3.811A  pdb=" N   TYR D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 675 through 680
      removed outlier: 3.814A  pdb=" N   LYS D 678 " --> pdb=" O   ASN D 675 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 681 through 688
      removed outlier: 4.184A  pdb=" N   TYR D 685 " --> pdb=" O   LEU D 681 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 4.055A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 714 through 725
      removed outlier: 4.592A  pdb=" N   ASN D 720 " --> pdb=" O   GLN D 716 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 729 through 743
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 4.036A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 787
    Processing helix  chain 'D' and resid 788 through 790
      No H-bonds generated for 'chain 'D' and resid 788 through 790'
    Processing helix  chain 'D' and resid 793 through 801
    Processing helix  chain 'D' and resid 803 through 816
    Processing helix  chain 'C' and resid 6 through 25
    Processing helix  chain 'C' and resid 30 through 36
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 42 through 51
      removed outlier: 4.063A  pdb=" N   MET C  46 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 64
      removed outlier: 4.205A  pdb=" N   TYR C  64 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 109
    Processing helix  chain 'C' and resid 110 through 112
      No H-bonds generated for 'chain 'C' and resid 110 through 112'
    Processing helix  chain 'C' and resid 119 through 127
    Processing helix  chain 'C' and resid 130 through 138
      removed outlier: 3.568A  pdb=" N   GLY C 138 " --> pdb=" O   ARG C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 150
    Processing helix  chain 'C' and resid 521 through 530
    Processing helix  chain 'C' and resid 535 through 554
      removed outlier: 3.534A  pdb=" N   ILE C 545 " --> pdb=" O   PHE C 541 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 594 through 600
      removed outlier: 4.007A  pdb=" N   THR C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 601 through 608
      removed outlier: 3.522A  pdb=" N   VAL C 605 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 618 through 628
    Processing helix  chain 'C' and resid 639 through 652
    Processing helix  chain 'C' and resid 654 through 658
    Processing helix  chain 'C' and resid 662 through 670
      removed outlier: 3.924A  pdb=" N   TYR C 670 " --> pdb=" O   LEU C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 675 through 680
      removed outlier: 3.954A  pdb=" N   LYS C 678 " --> pdb=" O   ASN C 675 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 681 through 688
      removed outlier: 4.049A  pdb=" N   TYR C 685 " --> pdb=" O   LEU C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 698 through 714
      removed outlier: 3.553A  pdb=" N   MET C 702 " --> pdb=" O   THR C 698 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASP C 708 " --> pdb=" O   TYR C 704 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL C 709 " --> pdb=" O   ALA C 705 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 714 through 724
      removed outlier: 4.174A  pdb=" N   ASN C 720 " --> pdb=" O   GLN C 716 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 729 through 743
    Processing helix  chain 'C' and resid 746 through 773
      removed outlier: 4.047A  pdb=" N   THR C 773 " --> pdb=" O   LYS C 769 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 780 through 787
      removed outlier: 3.545A  pdb=" N   ARG C 785 " --> pdb=" O   ASN C 781 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 788 through 790
      No H-bonds generated for 'chain 'C' and resid 788 through 790'
    Processing helix  chain 'C' and resid 793 through 801
    Processing helix  chain 'C' and resid 803 through 816
    Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'D' and resid 117 through 118
    Processing sheet with id=AA3, first strand: chain 'D' and resid 530 through 533
      removed outlier: 3.549A  pdb=" N   ILE D 576 " --> pdb=" O   PHE D 588 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA5, first strand: chain 'C' and resid 117 through 118
    Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 588
      removed outlier: 3.780A  pdb=" N   ILE C 576 " --> pdb=" O   PHE C 588 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   PHE C 637 " --> pdb=" O   VAL C 611 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   LYS C 613 " --> pdb=" O   PHE C 637 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1482 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      74 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      53 stacking parallelities
  Total time for adding SS restraints: 1.53

  Time building geometry restraints manager: 1.00 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.13 -     1.27: 1301
        1.27 -     1.40: 2123
        1.40 -     1.54: 4917
        1.54 -     1.68: 245
        1.68 -     1.81: 44
  Bond restraints: 8630
  Sorted by residual:
  bond pdb=" C   HIS C  31 "
       pdb=" O   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.236  1.133  0.103 1.26e-02 6.30e+03 6.71e+01
  bond pdb=" CA  HIS C  31 "
       pdb=" C   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.523  1.477  0.046 1.35e-02 5.49e+03 1.14e+01
  bond pdb=" O3'   A E  32 "
       pdb=" P     C E  33 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.50e-02 4.44e+03 1.09e+01
  bond pdb=" C   HIS C  31 "
       pdb=" N   ASP C  32 "
    ideal  model  delta    sigma   weight residual
    1.335  1.295  0.039 1.36e-02 5.41e+03 8.40e+00
  bond pdb=" CA  HIS C  31 "
       pdb=" CB  HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.528  1.494  0.034 1.66e-02 3.63e+03 4.29e+00
  ... (remaining 8625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 12020
        2.56 -     5.12: 122
        5.12 -     7.67: 3
        7.67 -    10.23: 0
       10.23 -    12.79: 2
  Bond angle restraints: 12147
  Sorted by residual:
  angle pdb=" C3'   C E  33 "
        pdb=" C2'   C E  33 "
        pdb=" O2'   C E  33 "
      ideal   model   delta    sigma   weight residual
     110.70  123.49  -12.79 1.50e+00 4.44e-01 7.27e+01
  angle pdb=" O3'   C E  33 "
        pdb=" C3'   C E  33 "
        pdb=" C2'   C E  33 "
      ideal   model   delta    sigma   weight residual
     113.70  124.29  -10.59 1.50e+00 4.44e-01 4.98e+01
  angle pdb=" C4'   A F  10 "
        pdb=" C3'   A F  10 "
        pdb=" O3'   A F  10 "
      ideal   model   delta    sigma   weight residual
     113.00  106.82    6.18 1.50e+00 4.44e-01 1.70e+01
  angle pdb=" CA  HIS C  31 "
        pdb=" C   HIS C  31 "
        pdb=" N   ASP C  32 "
      ideal   model   delta    sigma   weight residual
     117.72  122.19   -4.47 1.31e+00 5.83e-01 1.17e+01
  angle pdb=" O3'   A F  10 "
        pdb=" P     U F  11 "
        pdb=" O5'   U F  11 "
      ideal   model   delta    sigma   weight residual
     104.00   99.37    4.63 1.50e+00 4.44e-01 9.52e+00
  ... (remaining 12142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.84: 5020
       35.84 -    71.69: 205
       71.69 -   107.53: 14
      107.53 -   143.38: 0
      143.38 -   179.22: 2
  Dihedral angle restraints: 5241
    sinusoidal: 2240
      harmonic: 3001
  Sorted by residual:
  dihedral pdb=" C4'   C F  33 "
           pdb=" C3'   C F  33 "
           pdb=" O3'   C F  33 "
           pdb=" P     U F  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.78  179.22     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'   C E  33 "
           pdb=" C3'   C E  33 "
           pdb=" O3'   C E  33 "
           pdb=" P     U E  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   72.39  147.61     1      3.50e+01 8.16e-04 1.45e+01
  dihedral pdb=" CA  LYS C 659 "
           pdb=" C   LYS C 659 "
           pdb=" N   TYR C 660 "
           pdb=" CA  TYR C 660 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.61  -18.39     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 5238 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 1438
       0.083 -    0.166: 90
       0.166 -    0.249: 2
       0.249 -    0.332: 0
       0.332 -    0.415: 2
  Chirality restraints: 1532
  Sorted by residual:
  chirality pdb=" C2'   C E  33 "
            pdb=" C3'   C E  33 "
            pdb=" O2'   C E  33 "
            pdb=" C1'   C E  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.34   -0.41 2.00e-01 2.50e+01 4.30e+00
  chirality pdb=" C3'   C E  33 "
            pdb=" C4'   C E  33 "
            pdb=" O3'   C E  33 "
            pdb=" C2'   C E  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.11   -0.37 2.00e-01 2.50e+01 3.40e+00
  chirality pdb=" C3'   C F  33 "
            pdb=" C4'   C F  33 "
            pdb=" O3'   C F  33 "
            pdb=" C2'   C F  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.26   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1529 not shown)

  Planarity restraints: 1306
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  42 "   -0.085 2.00e-02 2.50e+03   3.51e-02 3.38e+01
        pdb=" N9    A F  42 "    0.042 2.00e-02 2.50e+03
        pdb=" C8    A F  42 "    0.023 2.00e-02 2.50e+03
        pdb=" N7    A F  42 "    0.012 2.00e-02 2.50e+03
        pdb=" C5    A F  42 "    0.009 2.00e-02 2.50e+03
        pdb=" C6    A F  42 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A F  42 "   -0.055 2.00e-02 2.50e+03
        pdb=" N1    A F  42 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A F  42 "    0.011 2.00e-02 2.50e+03
        pdb=" N3    A F  42 "    0.018 2.00e-02 2.50e+03
        pdb=" C4    A F  42 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  17 "    0.066 2.00e-02 2.50e+03   2.69e-02 1.99e+01
        pdb=" N9    A F  17 "   -0.034 2.00e-02 2.50e+03
        pdb=" C8    A F  17 "   -0.022 2.00e-02 2.50e+03
        pdb=" N7    A F  17 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    A F  17 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    A F  17 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A F  17 "    0.036 2.00e-02 2.50e+03
        pdb=" N1    A F  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A F  17 "   -0.012 2.00e-02 2.50e+03
        pdb=" N3    A F  17 "   -0.014 2.00e-02 2.50e+03
        pdb=" C4    A F  17 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G F   8 "   -0.057 2.00e-02 2.50e+03   2.26e-02 1.53e+01
        pdb=" N9    G F   8 "    0.032 2.00e-02 2.50e+03
        pdb=" C8    G F   8 "    0.023 2.00e-02 2.50e+03
        pdb=" N7    G F   8 "    0.010 2.00e-02 2.50e+03
        pdb=" C5    G F   8 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G F   8 "   -0.011 2.00e-02 2.50e+03
        pdb=" O6    G F   8 "   -0.023 2.00e-02 2.50e+03
        pdb=" N1    G F   8 "   -0.008 2.00e-02 2.50e+03
        pdb=" C2    G F   8 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G F   8 "    0.018 2.00e-02 2.50e+03
        pdb=" N3    G F   8 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    G F   8 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1303 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 611
        2.73 -     3.27: 8569
        3.27 -     3.82: 14276
        3.82 -     4.36: 15804
        4.36 -     4.90: 25222
  Nonbonded interactions: 64482
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN C 139 "
            pdb=" OP1   A F  30 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" O   THR D 773 "
            pdb=" NH1 ARG D 799 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   PHE C  42 "
            pdb=" OG1 THR C  43 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" NZ  LYS D 101 "
            pdb=" OD2 ASP D 153 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" O   THR C 158 "
            pdb=" OD1 ASP C 159 "
     model   vdw
     2.280 3.040
  ... (remaining 64477 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 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 5 through 81 or resid 92 through 816))
  selection = (chain 'D' and (resid 5 through 772 or (resid 773 through 801 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 802 or (resid 803 through 816 an \ 
d (name N or name CA or name C or name O or name CB ))))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.020
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
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      :  0.003   0.103   8630  Z= 0.209
  Angle     :  0.681  12.791  12147  Z= 0.388
  Chirality :  0.041   0.415   1532
  Planarity :  0.004   0.035   1306
  Dihedral  : 17.751 179.221   3277
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.27 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 21.03 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  1.18 (0.27), residues: 1008
  helix:  1.55 (0.21), residues: 603
  sheet: -0.62 (0.62), residues: 55
  loop : -0.24 (0.36), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 134 
 TYR   0.012   0.001   TYR C  64 
 PHE   0.023   0.001   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8630)
  covalent geometry    : angle       0.68117 (12147)
  hydrogen bonds       : bond        0.15358 (  586)
  hydrogen bonds       : angle       6.49537 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  728 GLN cc_start: 0.7544 (mt0) cc_final: 0.7340 (mt0)
REVERT: B  736 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7501 (ttp80)
REVERT: B  744 ARG cc_start: 0.7496 (ttp-170) cc_final: 0.7235 (ttp80)
REVERT: C  160 ASP cc_start: 0.4525 (t0) cc_final: 0.4295 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 123
  average time/residue: 0.0932
  time to fit residues: 15.8149
Evaluate side-chains
  108 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0470
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    7.9990
   overall best weight:    4.0086

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

Flipped N/Q/H residues before XYZ refinement:
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN
C 106 ASN
C 128 GLN
** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.144499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.119433 restraints weight = 19427.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.117829 restraints weight = 28495.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.118808 restraints weight = 24055.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.118775 restraints weight = 16740.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.118917 restraints weight = 18220.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8630  Z= 0.282
  Angle     :  0.653   7.793  12147  Z= 0.341
  Chirality :  0.042   0.178   1532
  Planarity :  0.004   0.034   1306
  Dihedral  : 15.893 175.116   2337
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.17 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 20.77 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  1.51 (0.27), residues: 1008
  helix:  1.88 (0.21), residues: 631
  sheet: -0.43 (0.62), residues: 57
  loop : -0.46 (0.37), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.019   0.002   TYR D 103 
 PHE   0.029   0.003   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.007   0.002   HIS C 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00610 ( 8630)
  covalent geometry    : angle       0.65296 (12147)
  hydrogen bonds       : bond        0.05309 (  586)
  hydrogen bonds       : angle       4.94309 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  746 MET cc_start: 0.6280 (ttt) cc_final: 0.6046 (mtm)
REVERT: D  160 ASP cc_start: 0.6786 (t70) cc_final: 0.6209 (t70)
REVERT: C   24 LYS cc_start: 0.7407 (tttm) cc_final: 0.7190 (tptm)
  outliers start: 21
  outliers final: 16
  residues processed: 126
  average time/residue: 0.0858
  time to fit residues: 14.8380
Evaluate side-chains
  118 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  155 PHE
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 82 optimal weight:   30.0000
   chunk 106 optimal weight:    7.9990
   chunk 28 optimal weight:    8.9990
   chunk 63 optimal weight:    0.8980
   chunk 68 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.148335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.123800 restraints weight = 19464.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.122589 restraints weight = 27135.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.123924 restraints weight = 22519.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.123520 restraints weight = 15727.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.123840 restraints weight = 15943.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8630  Z= 0.112
  Angle     :  0.482   7.048  12147  Z= 0.258
  Chirality :  0.036   0.169   1532
  Planarity :  0.003   0.035   1306
  Dihedral  : 15.691 171.605   2335
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.69 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.85 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  2.22 (0.27), residues: 1008
  helix:  2.33 (0.21), residues: 634
  sheet:  0.22 (0.64), residues: 55
  loop : -0.03 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 788 
 TYR   0.009   0.001   TYR C 161 
 PHE   0.017   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.001   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8630)
  covalent geometry    : angle       0.48211 (12147)
  hydrogen bonds       : bond        0.03459 (  586)
  hydrogen bonds       : angle       4.16281 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: C   19 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7713 (mt-10)
REVERT: C  126 ARG cc_start: 0.7197 (tmt170) cc_final: 0.6912 (tmt170)
  outliers start: 13
  outliers final: 9
  residues processed: 125
  average time/residue: 0.0816
  time to fit residues: 14.3863
Evaluate side-chains
  115 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:   50.0000
   chunk 66 optimal weight:    4.9990
   chunk 76 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 86 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 83 optimal weight:   40.0000
   chunk 20 optimal weight:    0.6980
   chunk 101 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.146368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.122052 restraints weight = 20030.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.121978 restraints weight = 25687.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.122549 restraints weight = 22410.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.122180 restraints weight = 16899.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.122437 restraints weight = 17539.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8630  Z= 0.164
  Angle     :  0.521   6.567  12147  Z= 0.275
  Chirality :  0.037   0.162   1532
  Planarity :  0.003   0.028   1306
  Dihedral  : 15.680 174.614   2335
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.68 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.05 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  2.20 (0.27), residues: 1008
  helix:  2.29 (0.21), residues: 637
  sheet:  0.08 (0.67), residues: 57
  loop :  0.02 (0.38), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.016   0.001   TYR D 789 
 PHE   0.020   0.002   PHE C  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS D 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8630)
  covalent geometry    : angle       0.52123 (12147)
  hydrogen bonds       : bond        0.03915 (  586)
  hydrogen bonds       : angle       4.20938 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  744 ARG cc_start: 0.7432 (mmm160) cc_final: 0.6904 (tpp-160)
REVERT: B  738 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7289 (mm-30)
REVERT: B  746 MET cc_start: 0.6862 (ttp) cc_final: 0.5903 (tpt)
REVERT: D  160 ASP cc_start: 0.6782 (t70) cc_final: 0.6178 (t70)
  outliers start: 16
  outliers final: 12
  residues processed: 124
  average time/residue: 0.0791
  time to fit residues: 13.8253
Evaluate side-chains
  113 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 66 optimal weight:    0.2980
   chunk 25 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:   50.0000
   chunk 105 optimal weight:    7.9990
   chunk 56 optimal weight:    0.4980
   chunk 77 optimal weight:    0.0370
   chunk 75 optimal weight:   50.0000
   chunk 90 optimal weight:    6.9990
   overall best weight:    1.5662

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

Flipped N/Q/H residues before XYZ refinement:
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.146985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.121969 restraints weight = 19907.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.120853 restraints weight = 27217.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.122276 restraints weight = 22551.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.121502 restraints weight = 15808.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.121776 restraints weight = 17796.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8630  Z= 0.135
  Angle     :  0.492   6.481  12147  Z= 0.260
  Chirality :  0.036   0.161   1532
  Planarity :  0.003   0.030   1306
  Dihedral  : 15.617 174.309   2335
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.38 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.56 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  2.31 (0.27), residues: 1008
  helix:  2.40 (0.20), residues: 637
  sheet:  0.31 (0.70), residues: 57
  loop : -0.01 (0.38), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 744 
 TYR   0.017   0.001   TYR D 789 
 PHE   0.020   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS C 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8630)
  covalent geometry    : angle       0.49246 (12147)
  hydrogen bonds       : bond        0.03538 (  586)
  hydrogen bonds       : angle       3.99982 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  738 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7291 (mm-30)
REVERT: B  746 MET cc_start: 0.6752 (ttp) cc_final: 0.5952 (tpt)
REVERT: C  149 MET cc_start: 0.5665 (mmt) cc_final: 0.5426 (tmm)
  outliers start: 14
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0829
  time to fit residues: 14.0957
Evaluate side-chains
  116 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 42 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 32 optimal weight:   40.0000
   chunk 52 optimal weight:    8.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.144266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.119577 restraints weight = 19704.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.118057 restraints weight = 28792.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.118953 restraints weight = 25412.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.119148 restraints weight = 17926.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.119281 restraints weight = 20840.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8630  Z= 0.230
  Angle     :  0.591   7.139  12147  Z= 0.310
  Chirality :  0.039   0.155   1532
  Planarity :  0.003   0.034   1306
  Dihedral  : 15.830 176.911   2335
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.88 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 24.36 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  1.93 (0.27), residues: 1008
  helix:  2.14 (0.20), residues: 638
  sheet:  0.21 (0.70), residues: 57
  loop : -0.28 (0.37), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.017   0.002   TYR D 789 
 PHE   0.027   0.003   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.005   0.001   HIS D 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 8630)
  covalent geometry    : angle       0.59115 (12147)
  hydrogen bonds       : bond        0.04555 (  586)
  hydrogen bonds       : angle       4.33701 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  746 MET cc_start: 0.6575 (ttp) cc_final: 0.5829 (tpt)
REVERT: C  163 MET cc_start: 0.6744 (tpp) cc_final: 0.6473 (mmm)
  outliers start: 18
  outliers final: 16
  residues processed: 118
  average time/residue: 0.0867
  time to fit residues: 14.5259
Evaluate side-chains
  113 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    0.0020
   chunk 95 optimal weight:    2.9990
   chunk 83 optimal weight:   30.0000
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 73 optimal weight:   30.0000
   chunk 48 optimal weight:    5.9990
   chunk 27 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.9992

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

Flipped N/Q/H residues before XYZ refinement:
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.147213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.120921 restraints weight = 19848.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.119575 restraints weight = 24217.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.120578 restraints weight = 21965.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.120509 restraints weight = 15350.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.120594 restraints weight = 14680.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8630  Z= 0.111
  Angle     :  0.473   6.407  12147  Z= 0.252
  Chirality :  0.035   0.156   1532
  Planarity :  0.003   0.038   1306
  Dihedral  : 15.642 175.310   2335
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.79 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 25.90 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  2.21 (0.27), residues: 1008
  helix:  2.27 (0.20), residues: 652
  sheet:  0.43 (0.72), residues: 57
  loop : -0.10 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 744 
 TYR   0.012   0.001   TYR D 789 
 PHE   0.019   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.001   0.001   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8630)
  covalent geometry    : angle       0.47305 (12147)
  hydrogen bonds       : bond        0.03354 (  586)
  hydrogen bonds       : angle       3.90596 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  746 MET cc_start: 0.6673 (ttp) cc_final: 0.5930 (tpt)
  outliers start: 12
  outliers final: 10
  residues processed: 111
  average time/residue: 0.0904
  time to fit residues: 14.1109
Evaluate side-chains
  114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 45 optimal weight:   20.0000
   chunk 28 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 82 optimal weight:   30.0000
   overall best weight:    4.3788

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.142907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.116569 restraints weight = 19547.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.114682 restraints weight = 28590.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.115815 restraints weight = 23909.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.115650 restraints weight = 16792.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.115861 restraints weight = 17823.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   8630  Z= 0.305
  Angle     :  0.663   9.081  12147  Z= 0.343
  Chirality :  0.041   0.155   1532
  Planarity :  0.004   0.053   1306
  Dihedral  : 15.955 179.870   2335
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.37 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 25.38 %
    Favored  : 70.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  1.78 (0.27), residues: 1008
  helix:  1.99 (0.20), residues: 637
  sheet:  0.14 (0.73), residues: 57
  loop : -0.26 (0.37), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 126 
 TYR   0.018   0.002   TYR D 103 
 PHE   0.028   0.003   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.006   0.002   HIS D 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 ( 8630)
  covalent geometry    : angle       0.66257 (12147)
  hydrogen bonds       : bond        0.05156 (  586)
  hydrogen bonds       : angle       4.49765 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  738 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7262 (mm-30)
REVERT: B  743 ASP cc_start: 0.8384 (m-30) cc_final: 0.7974 (m-30)
REVERT: B  746 MET cc_start: 0.6667 (ttp) cc_final: 0.5869 (tpt)
  outliers start: 15
  outliers final: 14
  residues processed: 115
  average time/residue: 0.0820
  time to fit residues: 13.5003
Evaluate side-chains
  114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   13 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 92 optimal weight:   40.0000
   chunk 103 optimal weight:    5.9990
   chunk 88 optimal weight:    7.9990
   chunk 32 optimal weight:   50.0000
   chunk 94 optimal weight:   10.0000
   chunk 74 optimal weight:   20.0000
   chunk 76 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0270
   chunk 97 optimal weight:   20.0000
   overall best weight:    4.4046

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.142301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.116018 restraints weight = 19504.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.114317 restraints weight = 27388.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.115415 restraints weight = 25051.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.115086 restraints weight = 16989.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.115271 restraints weight = 17437.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   8630  Z= 0.301
  Angle     :  0.657   8.809  12147  Z= 0.344
  Chirality :  0.041   0.159   1532
  Planarity :  0.004   0.044   1306
  Dihedral  : 16.101 178.150   2335
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.27 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.92 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  1.51 (0.27), residues: 1008
  helix:  1.74 (0.20), residues: 637
  sheet:  0.33 (0.77), residues: 55
  loop : -0.33 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.017   0.002   TYR D 103 
 PHE   0.026   0.003   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.005   0.001   HIS C 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 ( 8630)
  covalent geometry    : angle       0.65746 (12147)
  hydrogen bonds       : bond        0.05184 (  586)
  hydrogen bonds       : angle       4.59189 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: B  738 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7288 (mm-30)
REVERT: B  743 ASP cc_start: 0.8488 (m-30) cc_final: 0.8103 (m-30)
REVERT: B  746 MET cc_start: 0.6531 (ttp) cc_final: 0.5790 (tpt)
  outliers start: 16
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0801
  time to fit residues: 12.9101
Evaluate side-chains
  119 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  164 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 84 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 35 optimal weight:   40.0000
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.143684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.117282 restraints weight = 19480.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.115373 restraints weight = 26133.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.116371 restraints weight = 25658.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.116194 restraints weight = 16766.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.116333 restraints weight = 18053.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.4429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8630  Z= 0.217
  Angle     :  0.593   7.797  12147  Z= 0.312
  Chirality :  0.039   0.158   1532
  Planarity :  0.004   0.042   1306
  Dihedral  : 15.995 176.266   2335
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.17 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 27.95 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  1.68 (0.27), residues: 1008
  helix:  1.87 (0.21), residues: 639
  sheet:  0.34 (0.77), residues: 55
  loop : -0.27 (0.37), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.015   0.002   TYR D 103 
 PHE   0.020   0.003   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.008   0.001   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 8630)
  covalent geometry    : angle       0.59295 (12147)
  hydrogen bonds       : bond        0.04461 (  586)
  hydrogen bonds       : angle       4.37130 ( 1622)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: B  738 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7141 (mm-30)
REVERT: B  743 ASP cc_start: 0.8417 (m-30) cc_final: 0.7946 (m-30)
REVERT: B  746 MET cc_start: 0.6663 (ttp) cc_final: 0.6063 (tpt)
REVERT: C  163 MET cc_start: 0.6499 (mmt) cc_final: 0.6228 (mmt)
  outliers start: 14
  outliers final: 14
  residues processed: 117
  average time/residue: 0.0859
  time to fit residues: 14.0410
Evaluate side-chains
  118 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  164 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:   50.0000
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 84 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9980
   chunk 104 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0770
   chunk 5 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 102 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.147473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.122048 restraints weight = 19546.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.120611 restraints weight = 27227.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.121723 restraints weight = 23708.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.121740 restraints weight = 16627.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.121727 restraints weight = 17080.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8630  Z= 0.110
  Angle     :  0.510   9.286  12147  Z= 0.271
  Chirality :  0.035   0.153   1532
  Planarity :  0.003   0.035   1306
  Dihedral  : 15.782 175.106   2335
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.18 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 28.21 %
    Favored  : 68.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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 are not related in a simple way.
  whole:  2.12 (0.27), residues: 1008
  helix:  2.23 (0.21), residues: 640
  sheet:  0.06 (0.73), residues: 57
  loop : -0.03 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 744 
 TYR   0.010   0.001   TYR C  64 
 PHE   0.019   0.002   PHE C 144 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.000   HIS C 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 8630)
  covalent geometry    : angle       0.50958 (12147)
  hydrogen bonds       : bond        0.03309 (  586)
  hydrogen bonds       : angle       3.93997 ( 1622)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1263.69 seconds
wall clock time: 22 minutes 32.73 seconds (1352.73 seconds total)