Starting phenix.real_space_refine
on Sun Apr  5 02:31:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rwa_54305/04_2026/9rwa_54305.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rwa_54305/04_2026/9rwa_54305.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rwa_54305/04_2026/9rwa_54305.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rwa_54305/04_2026/9rwa_54305.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rwa_54305/04_2026/9rwa_54305.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rwa_54305/04_2026/9rwa_54305.cif"
  }
  resolution = 3.9
  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=   0.001
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      94      5.49       5
     S      27      5.16       5
     C    4303      2.51       5
     N    1278      2.21       5
     O    1677      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 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: 7379
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 355
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 88
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 62
    Chain: "B"
      Number of atoms: 351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 351
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 114
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 62
    Chain: "C"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1220
          Classifications: {'peptide': 154}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 149}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'ASP:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "D"
      Number of atoms: 3473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 3473
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 65}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 262
          Unresolved non-hydrogen angles: 328
          Unresolved non-hydrogen dihedrals: 218
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 5, 'ASN:plan1': 7, 'TYR:plan': 2, 'ASP:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 8, 'PHE:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 179
    Chain: "E"
      Number of atoms: 990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 990
          Classifications: {'RNA': 47}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 2, 'rna3p': 44}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 990
          Classifications: {'RNA': 47}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 19, 'rna3p_pyr': 26}
          Link IDs: {'rna2p': 2, 'rna3p': 44}
          Chain breaks: 1
  Time building chain proxies: 1.73, per 1000 atoms: 0.23
  Number of scatterers: 7379
  At special positions: 0
  Unit cell: (90.09, 93.73, 151.97, 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      27     16.00
     P      94     15.00
     O    1677      8.00
     N    1278      7.00
     C    4303      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: 0.75
  Conformation dependent library (CDL) restraints added in 226.0 milliseconds
  

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 5 sheets defined
      70.2% alpha, 7.8% beta
      36 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.904A  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 'C' and resid 6 through 25
      removed outlier: 3.919A  pdb=" N   LYS C  24 " --> pdb=" O   ARG C  20 " (cutoff:3.500A)
    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 44 through 51
    Processing helix  chain 'C' and resid 53 through 64
      removed outlier: 3.950A  pdb=" N   TYR C  64 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 112
      removed outlier: 3.517A  pdb=" N   PHE C 104 " --> pdb=" O   ALA C 100 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS C 107 " --> pdb=" O   TYR C 103 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   TYR C 111 " --> pdb=" O   LYS C 107 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLY C 112 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 126
      removed outlier: 3.594A  pdb=" N   LEU C 123 " --> pdb=" O   VAL C 119 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY C 124 " --> pdb=" O   ARG C 120 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   HIS C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 129
      No H-bonds generated for 'chain 'C' and resid 127 through 129'
    Processing helix  chain 'C' and resid 130 through 137
      removed outlier: 3.537A  pdb=" N   ILE C 136 " --> pdb=" O   GLN C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 151
    Processing helix  chain 'D' and resid 3 through 25
      removed outlier: 3.916A  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 51
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 111
      removed outlier: 3.625A  pdb=" N   TYR D 111 " --> pdb=" O   LYS D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.874A  pdb=" N   HIS D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 138
      removed outlier: 3.858A  pdb=" N   ILE D 136 " --> pdb=" O   GLN D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 150
    Processing helix  chain 'D' and resid 521 through 529
      removed outlier: 3.552A  pdb=" N   LEU D 527 " --> pdb=" O   LYS D 523 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   GLN D 528 " --> pdb=" O   ILE D 524 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ASN D 529 " --> pdb=" O   LYS D 525 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 4.219A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
      removed outlier: 3.560A  pdb=" N   VAL D 605 " --> pdb=" O   GLY D 601 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 617 through 629
      removed outlier: 4.455A  pdb=" N   ASP D 621 " --> pdb=" O   ASP D 617 " (cutoff:3.500A)
    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: 3.562A  pdb=" N   TYR D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 675 through 680
      removed outlier: 3.791A  pdb=" N   LYS D 678 " --> pdb=" O   ASN D 675 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 682 through 688
    Processing helix  chain 'D' and resid 690 through 694
      removed outlier: 4.401A  pdb=" N   LYS D 694 " --> pdb=" O   PHE D 691 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 713
      removed outlier: 4.295A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 717 through 725
      removed outlier: 3.569A  pdb=" N   ILE D 725 " --> pdb=" O   LEU D 721 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 729 through 744
      removed outlier: 4.622A  pdb=" N   GLN D 744 " --> pdb=" O   GLN D 740 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.617A  pdb=" N   ILE D 752 " --> pdb=" O   ASN D 748 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 786
    Processing helix  chain 'D' and resid 787 through 790
    Processing helix  chain 'D' and resid 793 through 801
    Processing helix  chain 'D' and resid 803 through 816
    Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'C' and resid 117 through 118
    Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA4, first strand: chain 'D' and resid 117 through 118
    Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 533
      removed outlier: 3.825A  pdb=" N   GLU D 584 " --> pdb=" O   THR D 580 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   ILE D 573 " --> pdb=" O   ILE D 565 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ILE D 565 " --> pdb=" O   ILE D 573 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   PHE D 637 " --> pdb=" O   VAL D 611 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LYS D 613 " --> pdb=" O   PHE D 637 " (cutoff:3.500A)

    367 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      88 hydrogen bonds
      160 hydrogen bond angles
      0 basepair planarities
      36 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 1.27

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1375
        1.33 -     1.45: 2186
        1.45 -     1.57: 3886
        1.57 -     1.69: 184
        1.69 -     1.81: 44
  Bond restraints: 7675
  Sorted by residual:
  bond pdb=" CA  ARG D  47 "
       pdb=" C   ARG D  47 "
    ideal  model  delta    sigma   weight residual
    1.524  1.462  0.061 1.27e-02 6.20e+03 2.33e+01
  bond pdb=" CA  ARG C 120 "
       pdb=" C   ARG C 120 "
    ideal  model  delta    sigma   weight residual
    1.523  1.490  0.033 1.30e-02 5.92e+03 6.62e+00
  bond pdb=" C   GLU C  45 "
       pdb=" O   GLU C  45 "
    ideal  model  delta    sigma   weight residual
    1.237  1.211  0.026 1.17e-02 7.31e+03 4.90e+00
  bond pdb=" C2'   C F  42 "
       pdb=" C1'   C F  42 "
    ideal  model  delta    sigma   weight residual
    1.529  1.559 -0.030 1.50e-02 4.44e+03 3.93e+00
  bond pdb=" C   ARG D  47 "
       pdb=" O   ARG D  47 "
    ideal  model  delta    sigma   weight residual
    1.236  1.214  0.022 1.15e-02 7.56e+03 3.77e+00
  ... (remaining 7670 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 10323
        1.65 -     3.30: 434
        3.30 -     4.94: 40
        4.94 -     6.59: 9
        6.59 -     8.24: 2
  Bond angle restraints: 10808
  Sorted by residual:
  angle pdb=" O4'   C F  42 "
        pdb=" C1'   C F  42 "
        pdb=" N1    C F  42 "
      ideal   model   delta    sigma   weight residual
     108.50  116.74   -8.24 1.50e+00 4.44e-01 3.02e+01
  angle pdb=" C2'   C F  42 "
        pdb=" C1'   C F  42 "
        pdb=" N1    C F  42 "
      ideal   model   delta    sigma   weight residual
     112.00  105.93    6.07 1.50e+00 4.44e-01 1.64e+01
  angle pdb=" O4'   U F  40 "
        pdb=" C1'   U F  40 "
        pdb=" N1    U F  40 "
      ideal   model   delta    sigma   weight residual
     108.50  114.40   -5.90 1.50e+00 4.44e-01 1.55e+01
  angle pdb=" C5'   U F  40 "
        pdb=" C4'   U F  40 "
        pdb=" O4'   U F  40 "
      ideal   model   delta    sigma   weight residual
     109.80  115.48   -5.68 1.50e+00 4.44e-01 1.43e+01
  angle pdb=" N   ARG D  47 "
        pdb=" CA  ARG D  47 "
        pdb=" CB  ARG D  47 "
      ideal   model   delta    sigma   weight residual
     110.01  114.93   -4.92 1.45e+00 4.76e-01 1.15e+01
  ... (remaining 10803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.12: 4331
       26.12 -    52.24: 332
       52.24 -    78.35: 114
       78.35 -   104.47: 14
      104.47 -   130.59: 2
  Dihedral angle restraints: 4793
    sinusoidal: 2677
      harmonic: 2116
  Sorted by residual:
  dihedral pdb=" O4'   C F  42 "
           pdb=" C2'   C F  42 "
           pdb=" C1'   C F  42 "
           pdb=" C3'   C F  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -9.21   34.21     1      8.00e+00 1.56e-02 2.60e+01
  dihedral pdb=" C4'   C F  42 "
           pdb=" O4'   C F  42 "
           pdb=" C1'   C F  42 "
           pdb=" C2'   C F  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -30.62   33.62     1      8.00e+00 1.56e-02 2.51e+01
  dihedral pdb=" C4'   U F  41 "
           pdb=" O4'   U F  41 "
           pdb=" C1'   U F  41 "
           pdb=" C2'   U F  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -18.91   21.91     1      8.00e+00 1.56e-02 1.08e+01
  ... (remaining 4790 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1033
       0.040 -    0.079: 202
       0.079 -    0.119: 85
       0.119 -    0.158: 11
       0.158 -    0.198: 2
  Chirality restraints: 1333
  Sorted by residual:
  chirality pdb=" C3'   U F  18 "
            pdb=" C4'   U F  18 "
            pdb=" O3'   U F  18 "
            pdb=" C2'   U F  18 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.68    0.20 2.00e-01 2.50e+01 9.81e-01
  chirality pdb=" C3'   A F  44 "
            pdb=" C4'   A F  44 "
            pdb=" O3'   A F  44 "
            pdb=" C2'   A F  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.65    0.17 2.00e-01 2.50e+01 7.44e-01
  chirality pdb=" C1'   G F  43 "
            pdb=" O4'   G F  43 "
            pdb=" C2'   G F  43 "
            pdb=" N9    G F  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.61   -0.16 2.00e-01 2.50e+01 6.08e-01
  ... (remaining 1330 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C F  42 "   -0.149 2.00e-02 2.50e+03   7.06e-02 1.12e+02
        pdb=" N1    C F  42 "    0.081 2.00e-02 2.50e+03
        pdb=" C2    C F  42 "    0.030 2.00e-02 2.50e+03
        pdb=" O2    C F  42 "    0.031 2.00e-02 2.50e+03
        pdb=" N3    C F  42 "    0.016 2.00e-02 2.50e+03
        pdb=" C4    C F  42 "    0.019 2.00e-02 2.50e+03
        pdb=" N4    C F  42 "   -0.103 2.00e-02 2.50e+03
        pdb=" C5    C F  42 "    0.030 2.00e-02 2.50e+03
        pdb=" C6    C F  42 "    0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  16 "   -0.083 2.00e-02 2.50e+03   3.52e-02 3.41e+01
        pdb=" N9    A F  16 "    0.028 2.00e-02 2.50e+03
        pdb=" C8    A F  16 "    0.031 2.00e-02 2.50e+03
        pdb=" N7    A F  16 "    0.018 2.00e-02 2.50e+03
        pdb=" C5    A F  16 "    0.010 2.00e-02 2.50e+03
        pdb=" C6    A F  16 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A F  16 "   -0.062 2.00e-02 2.50e+03
        pdb=" N1    A F  16 "    0.005 2.00e-02 2.50e+03
        pdb=" C2    A F  16 "    0.015 2.00e-02 2.50e+03
        pdb=" N3    A F  16 "    0.018 2.00e-02 2.50e+03
        pdb=" C4    A F  16 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  13 "   -0.084 2.00e-02 2.50e+03   3.44e-02 3.26e+01
        pdb=" N9    A F  13 "    0.033 2.00e-02 2.50e+03
        pdb=" C8    A F  13 "    0.025 2.00e-02 2.50e+03
        pdb=" N7    A F  13 "    0.016 2.00e-02 2.50e+03
        pdb=" C5    A F  13 "    0.010 2.00e-02 2.50e+03
        pdb=" C6    A F  13 "    0.001 2.00e-02 2.50e+03
        pdb=" N6    A F  13 "   -0.053 2.00e-02 2.50e+03
        pdb=" N1    A F  13 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    A F  13 "    0.012 2.00e-02 2.50e+03
        pdb=" N3    A F  13 "    0.024 2.00e-02 2.50e+03
        pdb=" C4    A F  13 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1575
        2.78 -     3.31: 7535
        3.31 -     3.84: 13034
        3.84 -     4.37: 14550
        4.37 -     4.90: 22602
  Nonbonded interactions: 59296
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG D 782 "
            pdb=" OP1   U E  18 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" NH1 ARG C  10 "
            pdb=" OH  TYR C  64 "
     model   vdw
     2.315 3.120
  nonbonded pdb=" NH2 ARG C  28 "
            pdb=" OD2 ASP C  32 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O   ASP D 102 "
            pdb=" OD1 ASP D 102 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" O   GLY D 601 "
            pdb=" OG1 THR D 604 "
     model   vdw
     2.369 3.040
  ... (remaining 59291 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' and (resid 695 through 729 or (resid 730 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 731 through 747))
  selection = chain 'B'
}
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:             3.030
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.160
  Find NCS groups from input model:        0.040
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6693
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7675  Z= 0.219
  Angle     :  0.729   8.241  10808  Z= 0.419
  Chirality :  0.039   0.198   1333
  Planarity :  0.005   0.071   1048
  Dihedral  : 19.311 130.591   3417
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  2.97 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.50 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.23 (0.32), residues: 706
  helix:  1.51 (0.25), residues: 430
  sheet: -1.66 (0.77), residues: 43
  loop :  0.15 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 120 
 TYR   0.032   0.001   TYR D 670 
 PHE   0.011   0.001   PHE D  16 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 7675)
  covalent geometry    : angle       0.72885 (10808)
  hydrogen bonds       : bond        0.19442 (  455)
  hydrogen bonds       : angle       6.97259 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  717 LYS cc_start: 0.8011 (tppt) cc_final: 0.7772 (mmmm)
REVERT: B  728 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7643 (mm-40)
REVERT: B  738 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: D  602 LEU cc_start: 0.7827 (tp) cc_final: 0.7609 (tp)
REVERT: D  730 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6629 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1251
  time to fit residues: 18.6560
Evaluate side-chains
  105 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
D 128 GLN
D 643 HIS
D 647 GLN
D 720 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.158418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.124724 restraints weight = 14797.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.123281 restraints weight = 17297.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.124282 restraints weight = 15405.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.125102 restraints weight = 11203.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.125202 restraints weight = 11045.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7675  Z= 0.198
  Angle     :  0.617   8.876  10808  Z= 0.318
  Chirality :  0.038   0.198   1333
  Planarity :  0.005   0.049   1048
  Dihedral  : 18.288 124.292   2222
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.98 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 19.11 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  1.58 (0.32), residues: 706
  helix:  1.87 (0.24), residues: 440
  sheet: -1.74 (0.75), residues: 37
  loop :  0.03 (0.43), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 736 
 TYR   0.014   0.002   TYR D 626 
 PHE   0.012   0.002   PHE C  60 
 TRP   0.001   0.000   TRP D 692 
 HIS   0.004   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 7675)
  covalent geometry    : angle       0.61653 (10808)
  hydrogen bonds       : bond        0.05508 (  455)
  hydrogen bonds       : angle       4.77141 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  163 MET cc_start: 0.6007 (OUTLIER) cc_final: 0.4987 (tmm)
REVERT: D  796 GLU cc_start: 0.6271 (mt-10) cc_final: 0.5559 (mm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 121
  average time/residue: 0.1071
  time to fit residues: 16.5060
Evaluate side-chains
  107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue  163 MET
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  661 ILE
Chi-restraints excluded: chain D residue  717 LEU
Chi-restraints excluded: chain D residue  793 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 68 optimal weight:    0.4980
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 58 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 44 optimal weight:   20.0000
   chunk 57 optimal weight:    0.3980
   chunk 52 optimal weight:    0.0370
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.5258

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.163086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.126928 restraints weight = 15133.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.128362 restraints weight = 12301.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.129021 restraints weight = 9606.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.128792 restraints weight = 7506.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.129189 restraints weight = 7228.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7675  Z= 0.115
  Angle     :  0.499   7.348  10808  Z= 0.256
  Chirality :  0.033   0.136   1333
  Planarity :  0.003   0.041   1048
  Dihedral  : 18.153 126.298   2222
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.27 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.46 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.33), residues: 706
  helix:  2.33 (0.24), residues: 444
  sheet: -1.66 (0.75), residues: 37
  loop :  0.33 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  94 
 TYR   0.010   0.001   TYR D 656 
 PHE   0.017   0.002   PHE D 629 
 TRP   0.001   0.001   TRP D 692 
 HIS   0.004   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7675)
  covalent geometry    : angle       0.49875 (10808)
  hydrogen bonds       : bond        0.04070 (  455)
  hydrogen bonds       : angle       4.12836 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 GLU cc_start: 0.7859 (tp30) cc_final: 0.7628 (tp30)
REVERT: A  717 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7833 (tttt)
REVERT: B  735 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: C  163 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5284 (tmm)
REVERT: D  561 ASP cc_start: 0.5028 (t0) cc_final: 0.4378 (t0)
REVERT: D  785 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7982 (mtm110)
  outliers start: 12
  outliers final: 6
  residues processed: 121
  average time/residue: 0.1160
  time to fit residues: 17.8537
Evaluate side-chains
  106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  163 MET
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  604 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 728 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.160645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.124732 restraints weight = 15116.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.124863 restraints weight = 12123.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.125700 restraints weight = 11605.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.126189 restraints weight = 8116.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.126464 restraints weight = 7759.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7675  Z= 0.157
  Angle     :  0.545   9.718  10808  Z= 0.277
  Chirality :  0.035   0.133   1333
  Planarity :  0.004   0.041   1048
  Dihedral  : 18.238 127.451   2222
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.56 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.62 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.00 (0.32), residues: 706
  helix:  2.14 (0.24), residues: 442
  sheet: -1.58 (0.84), residues: 32
  loop :  0.24 (0.44), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 120 
 TYR   0.009   0.001   TYR D 656 
 PHE   0.010   0.001   PHE C  60 
 TRP   0.004   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7675)
  covalent geometry    : angle       0.54543 (10808)
  hydrogen bonds       : bond        0.04635 (  455)
  hydrogen bonds       : angle       4.08897 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  735 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: C   67 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7627 (mt)
  outliers start: 16
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0903
  time to fit residues: 12.4302
Evaluate side-chains
  102 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain B residue  739 GLU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  766 LEU
Chi-restraints excluded: chain D residue  793 THR
Chi-restraints excluded: chain D residue  800 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 13 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 71 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 728 GLN
C 125 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.161638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.126595 restraints weight = 15237.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.124868 restraints weight = 14290.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.126402 restraints weight = 12534.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.126475 restraints weight = 8671.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.126530 restraints weight = 9515.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7675  Z= 0.121
  Angle     :  0.493   9.341  10808  Z= 0.250
  Chirality :  0.033   0.188   1333
  Planarity :  0.003   0.042   1048
  Dihedral  : 18.217 132.974   2222
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.70 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.01 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.09 (0.33), residues: 706
  helix:  2.18 (0.24), residues: 449
  sheet: -1.51 (0.84), residues: 32
  loop :  0.30 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  94 
 TYR   0.009   0.001   TYR D 789 
 PHE   0.011   0.001   PHE D 629 
 TRP   0.001   0.000   TRP D 692 
 HIS   0.003   0.001   HIS D 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7675)
  covalent geometry    : angle       0.49301 (10808)
  hydrogen bonds       : bond        0.04000 (  455)
  hydrogen bonds       : angle       3.87049 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  717 LYS cc_start: 0.8292 (mtpp) cc_final: 0.8026 (ttmt)
REVERT: B  735 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: C   67 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7643 (mt)
REVERT: D  109 LEU cc_start: 0.7405 (mt) cc_final: 0.7134 (mp)
REVERT: D  561 ASP cc_start: 0.5214 (OUTLIER) cc_final: 0.4559 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 105
  average time/residue: 0.0983
  time to fit residues: 13.4318
Evaluate side-chains
  103 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain B residue  739 GLU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  561 ASP
Chi-restraints excluded: chain D residue  602 LEU
Chi-restraints excluded: chain D residue  766 LEU
Chi-restraints excluded: chain D residue  793 THR
Chi-restraints excluded: chain D residue  800 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 42 optimal weight:   50.0000
   chunk 62 optimal weight:    0.5980
   chunk 34 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0370
   chunk 51 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   chunk 53 optimal weight:    0.8980
   chunk 64 optimal weight:    8.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
A 728 GLN
B 729 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.163416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.128636 restraints weight = 15117.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.126948 restraints weight = 14147.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.128432 restraints weight = 12722.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.128435 restraints weight = 8777.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.128543 restraints weight = 9393.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7675  Z= 0.101
  Angle     :  0.480   8.895  10808  Z= 0.240
  Chirality :  0.032   0.157   1333
  Planarity :  0.003   0.041   1048
  Dihedral  : 18.165 125.355   2222
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.84 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 22.39 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.23 (0.33), residues: 706
  helix:  2.29 (0.24), residues: 451
  sheet: -1.44 (0.82), residues: 32
  loop :  0.32 (0.45), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 120 
 TYR   0.018   0.001   TYR D 670 
 PHE   0.008   0.001   PHE D 104 
 TRP   0.001   0.000   TRP D 692 
 HIS   0.004   0.001   HIS D 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 7675)
  covalent geometry    : angle       0.48026 (10808)
  hydrogen bonds       : bond        0.03651 (  455)
  hydrogen bonds       : angle       3.68161 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  717 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7993 (ttmt)
REVERT: B  735 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: D  109 LEU cc_start: 0.7386 (mt) cc_final: 0.7083 (mp)
REVERT: D  561 ASP cc_start: 0.5259 (OUTLIER) cc_final: 0.4570 (t0)
REVERT: D  615 ILE cc_start: 0.8847 (tp) cc_final: 0.8330 (mp)
REVERT: D  800 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6875 (mm)
  outliers start: 14
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0828
  time to fit residues: 11.4572
Evaluate side-chains
  106 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  561 ASP
Chi-restraints excluded: chain D residue  793 THR
Chi-restraints excluded: chain D residue  800 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 73 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B 729 GLN
** D 608 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 = 0.4186 r_free = 0.4186 target = 0.160964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.125708 restraints weight = 15370.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.124687 restraints weight = 14935.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.125948 restraints weight = 13374.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.126329 restraints weight = 9570.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.126423 restraints weight = 9998.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7675  Z= 0.149
  Angle     :  0.540  14.751  10808  Z= 0.269
  Chirality :  0.034   0.141   1333
  Planarity :  0.004   0.041   1048
  Dihedral  : 18.190 120.883   2222
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.98 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.04 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.05 (0.32), residues: 706
  helix:  2.16 (0.24), residues: 449
  sheet: -1.50 (0.81), residues: 32
  loop :  0.24 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 788 
 TYR   0.009   0.001   TYR D 685 
 PHE   0.014   0.002   PHE C 104 
 TRP   0.003   0.001   TRP D 692 
 HIS   0.009   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7675)
  covalent geometry    : angle       0.54048 (10808)
  hydrogen bonds       : bond        0.04246 (  455)
  hydrogen bonds       : angle       3.82108 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  717 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8072 (ttmt)
REVERT: A  736 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7494 (ttm-80)
REVERT: B  735 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: C   67 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7708 (mt)
REVERT: D   69 LEU cc_start: 0.8617 (tp) cc_final: 0.8121 (tt)
REVERT: D  109 LEU cc_start: 0.7613 (mt) cc_final: 0.7274 (mp)
REVERT: D  561 ASP cc_start: 0.4956 (OUTLIER) cc_final: 0.4209 (m-30)
  outliers start: 19
  outliers final: 14
  residues processed: 108
  average time/residue: 0.0961
  time to fit residues: 13.4978
Evaluate side-chains
  108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain B residue  739 GLU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  142 LYS
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  561 ASP
Chi-restraints excluded: chain D residue  602 LEU
Chi-restraints excluded: chain D residue  766 LEU
Chi-restraints excluded: chain D residue  793 THR
Chi-restraints excluded: chain D residue  800 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0270
   chunk 32 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0040
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.5452

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

Flipped N/Q/H residues before XYZ refinement:
** D 608 HIS ** 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 = 0.4182 r_free = 0.4182 target = 0.161142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.127781 restraints weight = 15452.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.126326 restraints weight = 18393.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.127638 restraints weight = 18155.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.127862 restraints weight = 12238.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.128154 restraints weight = 12402.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7675  Z= 0.109
  Angle     :  0.527  15.248  10808  Z= 0.258
  Chirality :  0.033   0.147   1333
  Planarity :  0.003   0.042   1048
  Dihedral  : 18.126 117.637   2222
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.84 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 22.20 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.33), residues: 706
  helix:  2.32 (0.24), residues: 448
  sheet: -1.48 (0.80), residues: 32
  loop :  0.27 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 120 
 TYR   0.007   0.001   TYR D 685 
 PHE   0.008   0.001   PHE C 104 
 TRP   0.001   0.000   TRP D 692 
 HIS   0.004   0.001   HIS D 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7675)
  covalent geometry    : angle       0.52710 (10808)
  hydrogen bonds       : bond        0.03692 (  455)
  hydrogen bonds       : angle       3.66257 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  717 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7956 (ttmt)
REVERT: C   67 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7638 (mt)
REVERT: C  163 MET cc_start: 0.5183 (mpp) cc_final: 0.4889 (tmm)
REVERT: C  164 LEU cc_start: 0.1392 (OUTLIER) cc_final: 0.0969 (mm)
REVERT: D   69 LEU cc_start: 0.8643 (tp) cc_final: 0.8205 (tt)
REVERT: D  109 LEU cc_start: 0.7304 (mt) cc_final: 0.7051 (mp)
REVERT: D  561 ASP cc_start: 0.4683 (OUTLIER) cc_final: 0.4090 (m-30)
  outliers start: 20
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1039
  time to fit residues: 15.1811
Evaluate side-chains
  108 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain B residue  739 GLU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  142 LYS
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  561 ASP
Chi-restraints excluded: chain D residue  766 LEU
Chi-restraints excluded: chain D residue  793 THR
Chi-restraints excluded: chain D residue  800 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 42 optimal weight:   40.0000
   chunk 41 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 50 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 66 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0040
   overall best weight:    0.8394

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

Flipped N/Q/H residues before XYZ refinement:
B 729 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.160040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.129258 restraints weight = 14961.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.127681 restraints weight = 23329.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.129110 restraints weight = 22109.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.129174 restraints weight = 16001.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.129286 restraints weight = 18305.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7675  Z= 0.130
  Angle     :  0.536   9.105  10808  Z= 0.266
  Chirality :  0.033   0.141   1333
  Planarity :  0.004   0.041   1048
  Dihedral  : 18.130 116.317   2222
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.84 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.17 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  2.18 (0.33), residues: 706
  helix:  2.30 (0.24), residues: 448
  sheet: -1.55 (0.80), residues: 32
  loop :  0.24 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 788 
 TYR   0.008   0.001   TYR D 685 
 PHE   0.012   0.001   PHE C 104 
 TRP   0.002   0.001   TRP D 692 
 HIS   0.003   0.001   HIS D 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7675)
  covalent geometry    : angle       0.53646 (10808)
  hydrogen bonds       : bond        0.03994 (  455)
  hydrogen bonds       : angle       3.70305 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7272 (ttm-80)
REVERT: C   67 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7652 (mt)
REVERT: C  164 LEU cc_start: 0.1388 (OUTLIER) cc_final: 0.1010 (mm)
REVERT: D  109 LEU cc_start: 0.7522 (mt) cc_final: 0.7176 (mp)
REVERT: D  561 ASP cc_start: 0.4543 (OUTLIER) cc_final: 0.3990 (m-30)
  outliers start: 16
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1021
  time to fit residues: 13.7237
Evaluate side-chains
  107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain B residue  739 GLU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  561 ASP
Chi-restraints excluded: chain D residue  766 LEU
Chi-restraints excluded: chain D residue  800 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 59 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.160510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.128914 restraints weight = 15159.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.127169 restraints weight = 21582.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.128397 restraints weight = 19863.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.128415 restraints weight = 14164.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.128724 restraints weight = 14480.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7675  Z= 0.125
  Angle     :  0.558  15.211  10808  Z= 0.274
  Chirality :  0.033   0.144   1333
  Planarity :  0.004   0.041   1048
  Dihedral  : 18.131 115.514   2222
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.84 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.97 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.33), residues: 706
  helix:  2.34 (0.24), residues: 448
  sheet: -1.55 (0.79), residues: 32
  loop :  0.25 (0.45), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 788 
 TYR   0.008   0.001   TYR D 685 
 PHE   0.010   0.001   PHE C 104 
 TRP   0.001   0.000   TRP D 692 
 HIS   0.003   0.001   HIS D 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7675)
  covalent geometry    : angle       0.55764 (10808)
  hydrogen bonds       : bond        0.03883 (  455)
  hydrogen bonds       : angle       3.70825 ( 1216)

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

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

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1412 Ramachandran restraints generated.
    706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  736 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7210 (ttm-80)
REVERT: B  735 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7616 (tm-30)
REVERT: C   67 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7734 (mt)
REVERT: C  164 LEU cc_start: 0.1793 (OUTLIER) cc_final: 0.1564 (mm)
REVERT: D  109 LEU cc_start: 0.7520 (mt) cc_final: 0.7197 (mp)
REVERT: D  561 ASP cc_start: 0.4551 (OUTLIER) cc_final: 0.3966 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 104
  average time/residue: 0.0990
  time to fit residues: 13.3724
Evaluate side-chains
  107 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  736 ARG
Chi-restraints excluded: chain B residue  739 GLU
Chi-restraints excluded: chain C residue   15 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  148 LEU
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  164 LEU
Chi-restraints excluded: chain D residue  141 ILE
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain D residue  561 ASP
Chi-restraints excluded: chain D residue  740 GLN
Chi-restraints excluded: chain D residue  766 LEU
Chi-restraints excluded: chain D residue  800 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 13 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 78 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.160712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.129152 restraints weight = 15009.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.127678 restraints weight = 27263.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.129199 restraints weight = 21386.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.129387 restraints weight = 16096.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.129772 restraints weight = 15038.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7675  Z= 0.120
  Angle     :  0.556  16.372  10808  Z= 0.271
  Chirality :  0.032   0.146   1333
  Planarity :  0.003   0.041   1048
  Dihedral  : 18.117 114.790   2222
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  1.84 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 23.75 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.33), residues: 706
  helix:  2.34 (0.24), residues: 448
  sheet: -1.52 (0.79), residues: 32
  loop :  0.18 (0.44), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 788 
 TYR   0.008   0.001   TYR D 685 
 PHE   0.011   0.001   PHE D 629 
 TRP   0.001   0.000   TRP D 692 
 HIS   0.003   0.001   HIS D 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7675)
  covalent geometry    : angle       0.55570 (10808)
  hydrogen bonds       : bond        0.03800 (  455)
  hydrogen bonds       : angle       3.63908 ( 1216)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1280.33 seconds
wall clock time: 22 minutes 47.22 seconds (1367.22 seconds total)