Starting phenix.real_space_refine
on Thu Jul  2 11:26:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw1_54295/07_2026/9rw1_54295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw1_54295/07_2026/9rw1_54295.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw1_54295/07_2026/9rw1_54295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw1_54295/07_2026/9rw1_54295.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw1_54295/07_2026/9rw1_54295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw1_54295/07_2026/9rw1_54295.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      88      5.49       5
     S      24      5.16       5
     C    4841      2.51       5
     N    1526      2.21       5
     O    1887      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8366
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 412
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 412
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "D"
      Number of atoms: 2925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 2925
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 234}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          Chain breaks: 3
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 833
          Unresolved non-hydrogen angles: 1060
          Unresolved non-hydrogen dihedrals: 678
          Unresolved non-hydrogen chiralities: 82
          Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 16, 'TYR:plan': 9, 'ASP:plan': 14, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 11, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 438
    Chain: "C"
      Number of atoms: 2767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 2767
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 274}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448}
          Chain breaks: 3
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 981
          Unresolved non-hydrogen angles: 1242
          Unresolved non-hydrogen dihedrals: 801
          Unresolved non-hydrogen chiralities: 94
          Planarities with less than four sites: {'GLU:plan': 22, 'ASN:plan1': 17, 'TYR:plan': 12, 'ASP:plan': 16, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 15, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 512
    Chain: "E"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
    Chain: "F"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
  Time building chain proxies: 1.69, per 1000 atoms: 0.20
  Number of scatterers: 8366
  At special positions: 0
  Unit cell: (87.897, 91.074, 182.148, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      24     16.00
     P      88     15.00
     O    1887      8.00
     N    1526      7.00
     C    4841      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 334.5 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 6 sheets defined
      69.1% alpha, 6.4% beta
      35 base pairs and 53 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.598A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 747
    Processing helix  chain 'D' and resid 3 through 25
      removed outlier: 3.733A  pdb=" N   LYS D  24 " --> pdb=" O   ARG D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 36
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 43 through 50
    Processing helix  chain 'D' and resid 53 through 63
    Processing helix  chain 'D' and resid 95 through 110
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.939A  pdb=" N   HIS D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 129
    Processing helix  chain 'D' and resid 130 through 138
    Processing helix  chain 'D' and resid 140 through 151
    Processing helix  chain 'D' and resid 521 through 529
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 3.811A  pdb=" N   THR D 598 " --> pdb=" O   PRO D 594 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 601 through 608
    Processing helix  chain 'D' and resid 618 through 629
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 654 through 658
    Processing helix  chain 'D' and resid 662 through 670
      removed outlier: 3.811A  pdb=" N   TYR D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 675 through 680
      removed outlier: 3.814A  pdb=" N   LYS D 678 " --> pdb=" O   ASN D 675 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 681 through 688
      removed outlier: 4.184A  pdb=" N   TYR D 685 " --> pdb=" O   LEU D 681 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 4.055A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 714 through 725
      removed outlier: 4.592A  pdb=" N   ASN D 720 " --> pdb=" O   GLN D 716 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 729 through 743
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 4.036A  pdb=" N   THR D 773 " --> pdb=" O   LYS D 769 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 780 through 787
    Processing helix  chain 'D' and resid 788 through 790
      No H-bonds generated for 'chain 'D' and resid 788 through 790'
    Processing helix  chain 'D' and resid 793 through 801
    Processing helix  chain 'D' and resid 803 through 816
    Processing helix  chain 'C' and resid 6 through 25
    Processing helix  chain 'C' and resid 30 through 36
    Processing helix  chain 'C' and resid 37 through 39
      No H-bonds generated for 'chain 'C' and resid 37 through 39'
    Processing helix  chain 'C' and resid 42 through 51
      removed outlier: 4.063A  pdb=" N   MET C  46 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 64
      removed outlier: 4.205A  pdb=" N   TYR C  64 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 109
    Processing helix  chain 'C' and resid 110 through 112
      No H-bonds generated for 'chain 'C' and resid 110 through 112'
    Processing helix  chain 'C' and resid 119 through 127
    Processing helix  chain 'C' and resid 130 through 138
      removed outlier: 3.568A  pdb=" N   GLY C 138 " --> pdb=" O   ARG C 134 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 150
    Processing helix  chain 'C' and resid 521 through 530
    Processing helix  chain 'C' and resid 535 through 554
      removed outlier: 3.534A  pdb=" N   ILE C 545 " --> pdb=" O   PHE C 541 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 594 through 600
      removed outlier: 4.007A  pdb=" N   THR C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 601 through 608
      removed outlier: 3.522A  pdb=" N   VAL C 605 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 618 through 628
    Processing helix  chain 'C' and resid 639 through 652
    Processing helix  chain 'C' and resid 654 through 658
    Processing helix  chain 'C' and resid 662 through 670
      removed outlier: 3.924A  pdb=" N   TYR C 670 " --> pdb=" O   LEU C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 675 through 680
      removed outlier: 3.954A  pdb=" N   LYS C 678 " --> pdb=" O   ASN C 675 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 681 through 688
      removed outlier: 4.049A  pdb=" N   TYR C 685 " --> pdb=" O   LEU C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 698 through 714
      removed outlier: 3.553A  pdb=" N   MET C 702 " --> pdb=" O   THR C 698 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASP C 708 " --> pdb=" O   TYR C 704 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL C 709 " --> pdb=" O   ALA C 705 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 714 through 724
      removed outlier: 4.174A  pdb=" N   ASN C 720 " --> pdb=" O   GLN C 716 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 729 through 743
    Processing helix  chain 'C' and resid 746 through 773
      removed outlier: 4.047A  pdb=" N   THR C 773 " --> pdb=" O   LYS C 769 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 780 through 787
      removed outlier: 3.545A  pdb=" N   ARG C 785 " --> pdb=" O   ASN C 781 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 788 through 790
      No H-bonds generated for 'chain 'C' and resid 788 through 790'
    Processing helix  chain 'C' and resid 793 through 801
    Processing helix  chain 'C' and resid 803 through 816
    Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29
    Processing sheet with id=AA2, first strand: chain 'D' and resid 117 through 118
    Processing sheet with id=AA3, first strand: chain 'D' and resid 530 through 533
      removed outlier: 3.549A  pdb=" N   ILE D 576 " --> pdb=" O   PHE D 588 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 29
    Processing sheet with id=AA5, first strand: chain 'C' and resid 117 through 118
    Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 588
      removed outlier: 3.780A  pdb=" N   ILE C 576 " --> pdb=" O   PHE C 588 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   PHE C 637 " --> pdb=" O   VAL C 611 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   LYS C 613 " --> pdb=" O   PHE C 637 " (cutoff:3.500A)

    512 hydrogen bonds defined for protein.
    1482 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      74 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      35 basepair parallelities
      53 stacking parallelities
  Total time for adding SS restraints: 1.50

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1301
        1.27 -     1.40: 2123
        1.40 -     1.54: 4917
        1.54 -     1.68: 245
        1.68 -     1.81: 44
  Bond restraints: 8630
  Sorted by residual:
  bond pdb=" C   HIS C  31 "
       pdb=" O   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.236  1.133  0.103 1.26e-02 6.30e+03 6.71e+01
  bond pdb=" N1    C F   1 "
       pdb=" C6    C F   1 "
    ideal  model  delta    sigma   weight residual
    1.367  1.389 -0.022 6.00e-03 2.78e+04 1.38e+01
  bond pdb=" CA  HIS C  31 "
       pdb=" C   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.523  1.477  0.046 1.35e-02 5.49e+03 1.14e+01
  bond pdb=" O3'   A E  32 "
       pdb=" P     C E  33 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.50e-02 4.44e+03 1.09e+01
  bond pdb=" C   HIS C  31 "
       pdb=" N   ASP C  32 "
    ideal  model  delta    sigma   weight residual
    1.335  1.295  0.039 1.36e-02 5.41e+03 8.40e+00
  ... (remaining 8625 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 12020
        2.56 -     5.12: 122
        5.12 -     7.67: 3
        7.67 -    10.23: 0
       10.23 -    12.79: 2
  Bond angle restraints: 12147
  Sorted by residual:
  angle pdb=" C3'   C E  33 "
        pdb=" C2'   C E  33 "
        pdb=" O2'   C E  33 "
      ideal   model   delta    sigma   weight residual
     110.70  123.49  -12.79 1.50e+00 4.44e-01 7.27e+01
  angle pdb=" O3'   C E  33 "
        pdb=" C3'   C E  33 "
        pdb=" C2'   C E  33 "
      ideal   model   delta    sigma   weight residual
     113.70  124.29  -10.59 1.50e+00 4.44e-01 4.98e+01
  angle pdb=" N6    A F  31 "
        pdb=" C6    A F  31 "
        pdb=" N1    A F  31 "
      ideal   model   delta    sigma   weight residual
     118.60  115.03    3.57 6.00e-01 2.78e+00 3.54e+01
  angle pdb=" N6    A F  30 "
        pdb=" C6    A F  30 "
        pdb=" N1    A F  30 "
      ideal   model   delta    sigma   weight residual
     118.60  115.07    3.53 6.00e-01 2.78e+00 3.46e+01
  angle pdb=" N6    A F  37 "
        pdb=" C6    A F  37 "
        pdb=" N1    A F  37 "
      ideal   model   delta    sigma   weight residual
     118.60  115.34    3.26 6.00e-01 2.78e+00 2.96e+01
  ... (remaining 12142 not shown)

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

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

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

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 611
        2.73 -     3.27: 8569
        3.27 -     3.82: 14276
        3.82 -     4.36: 15804
        4.36 -     4.90: 25222
  Nonbonded interactions: 64482
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN C 139 "
            pdb=" OP1   A F  30 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" O   THR D 773 "
            pdb=" NH1 ARG D 799 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   PHE C  42 "
            pdb=" OG1 THR C  43 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" NZ  LYS D 101 "
            pdb=" OD2 ASP D 153 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" O   THR C 158 "
            pdb=" OD1 ASP C 159 "
     model   vdw
     2.280 3.040
  ... (remaining 64477 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 5 through 81 or resid 92 through 816))
  selection = (chain 'D' and (resid 5 through 772 or (resid 773 through 801 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 802 or (resid 803 through 816 an \ 
d (name N or name CA or name C or name O or name CB ))))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.620
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103   8630  Z= 0.301
  Angle     :  0.681  12.791  12147  Z= 0.632
  Chirality :  0.041   0.415   1532
  Planarity :  0.004   0.035   1306
  Dihedral  : 17.751 179.221   3277
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.27 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 21.03 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.27), residues: 1008
  helix:  1.55 (0.21), residues: 603
  sheet: -0.62 (0.62), residues: 55
  loop : -0.24 (0.36), residues: 350

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.30 ( 8630)
  covalent geometry    : angle       0.68119 /  0.63 (12147)
  hydrogen bonds       : bond        0.15358 / 10.44 (  586)
  hydrogen bonds       : angle       6.49537 /  4.63 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  728 GLN cc_start: 0.7544 (mt0) cc_final: 0.7340 (mt0)
REVERT: B  736 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7501 (ttp80)
REVERT: B  744 ARG cc_start: 0.7496 (ttp-170) cc_final: 0.7235 (ttp80)
REVERT: C  160 ASP cc_start: 0.4525 (t0) cc_final: 0.4295 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 123
  average time/residue: 0.0779
  time to fit residues: 13.3065
Evaluate side-chains
  108 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0470
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    4.0086

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 106 ASN
C 128 GLN
** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.145207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.119750 restraints weight = 19672.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.118144 restraints weight = 29181.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.119195 restraints weight = 23790.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.118980 restraints weight = 16140.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.119255 restraints weight = 17846.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   8630  Z= 0.262
  Angle     :  0.594   6.431  12147  Z= 0.343
  Chirality :  0.042   0.187   1532
  Planarity :  0.004   0.032   1306
  Dihedral  : 15.609 168.209   2337
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.78 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 19.23 %
    Favored  : 75.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.27), residues: 1008
  helix:  1.64 (0.20), residues: 631
  sheet: -0.42 (0.63), residues: 55
  loop : -0.39 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 744 
 TYR   0.017   0.002   TYR C  64 
 PHE   0.024   0.003   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.002   HIS D 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00561 /  0.26 ( 8630)
  covalent geometry    : angle       0.59430 /  0.34 (12147)
  hydrogen bonds       : bond        0.05780 /  3.93 (  586)
  hydrogen bonds       : angle       5.16528 /  3.69 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: B  730 LYS cc_start: 0.8223 (tttm) cc_final: 0.7898 (tttm)
  outliers start: 19
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0693
  time to fit residues: 11.5987
Evaluate side-chains
  114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain B residue  745 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 82 optimal weight:   50.0000
   chunk 106 optimal weight:   10.0000
   chunk 28 optimal weight:   40.0000
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 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 = 0.4193 r_free = 0.4193 target = 0.147640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.124020 restraints weight = 19499.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.124036 restraints weight = 27997.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.124914 restraints weight = 25613.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.124525 restraints weight = 18291.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.124826 restraints weight = 17651.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8630  Z= 0.138
  Angle     :  0.489   6.627  12147  Z= 0.286
  Chirality :  0.038   0.170   1532
  Planarity :  0.003   0.031   1306
  Dihedral  : 15.660 169.119   2335
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.28 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.28 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.27), residues: 1008
  helix:  2.07 (0.21), residues: 630
  sheet: -0.14 (0.64), residues: 55
  loop : -0.25 (0.38), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 788 
 TYR   0.016   0.001   TYR D 789 
 PHE   0.022   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS D 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.14 ( 8630)
  covalent geometry    : angle       0.48919 /  0.29 (12147)
  hydrogen bonds       : bond        0.04335 /  2.95 (  586)
  hydrogen bonds       : angle       4.65033 /  3.35 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 12
  residues processed: 124
  average time/residue: 0.0611
  time to fit residues: 10.8798
Evaluate side-chains
  116 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:   50.0000
   chunk 66 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 0 optimal weight:   30.0000
   chunk 86 optimal weight:    0.0370
   chunk 15 optimal weight:    2.9990
   chunk 83 optimal weight:   50.0000
   chunk 20 optimal weight:    0.6980
   chunk 101 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.9464

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 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 = 0.4180 r_free = 0.4180 target = 0.146478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.121220 restraints weight = 19800.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.120519 restraints weight = 28476.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.121611 restraints weight = 23759.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.121156 restraints weight = 16577.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.121405 restraints weight = 16558.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8630  Z= 0.157
  Angle     :  0.492   6.316  12147  Z= 0.285
  Chirality :  0.038   0.165   1532
  Planarity :  0.003   0.051   1306
  Dihedral  : 15.587 170.640   2335
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.68 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.56 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.27), residues: 1008
  helix:  2.04 (0.21), residues: 631
  sheet: -0.02 (0.66), residues: 55
  loop : -0.24 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 126 
 TYR   0.011   0.001   TYR C  64 
 PHE   0.024   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS D 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.16 ( 8630)
  covalent geometry    : angle       0.49220 /  0.29 (12147)
  hydrogen bonds       : bond        0.04357 /  2.98 (  586)
  hydrogen bonds       : angle       4.51100 /  3.28 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  160 ASP cc_start: 0.6603 (t70) cc_final: 0.6040 (t70)
  outliers start: 16
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0672
  time to fit residues: 11.2094
Evaluate side-chains
  117 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 25 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 27 optimal weight:   50.0000
   chunk 105 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 77 optimal weight:    7.9990
   chunk 75 optimal weight:   50.0000
   chunk 90 optimal weight:    6.9990
   overall best weight:    4.3188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 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 = 0.4151 r_free = 0.4151 target = 0.144277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.118925 restraints weight = 19486.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.117063 restraints weight = 29543.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.118076 restraints weight = 26237.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.118322 restraints weight = 18534.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.118431 restraints weight = 17167.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8630  Z= 0.288
  Angle     :  0.603   6.546  12147  Z= 0.340
  Chirality :  0.042   0.176   1532
  Planarity :  0.004   0.038   1306
  Dihedral  : 15.722 173.678   2335
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.08 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 22.56 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.45 (0.27), residues: 1008
  helix:  1.78 (0.21), residues: 632
  sheet: -0.24 (0.67), residues: 57
  loop : -0.39 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 126 
 TYR   0.018   0.002   TYR D 103 
 PHE   0.027   0.003   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.006   0.002   HIS D 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00626 /  0.29 ( 8630)
  covalent geometry    : angle       0.60332 /  0.34 (12147)
  hydrogen bonds       : bond        0.05425 /  3.72 (  586)
  hydrogen bonds       : angle       4.73475 /  3.45 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 19
  residues processed: 115
  average time/residue: 0.0714
  time to fit residues: 11.6302
Evaluate side-chains
  112 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   13 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  164 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 77 optimal weight:    0.0870
   chunk 49 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 42 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 65 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 32 optimal weight:   20.0000
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.3360

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 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 = 0.4188 r_free = 0.4188 target = 0.147120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.122492 restraints weight = 19422.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.120391 restraints weight = 26311.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.121548 restraints weight = 26599.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.121577 restraints weight = 16977.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.121788 restraints weight = 17831.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8630  Z= 0.129
  Angle     :  0.474   6.261  12147  Z= 0.276
  Chirality :  0.037   0.155   1532
  Planarity :  0.003   0.036   1306
  Dihedral  : 15.752 172.249   2335
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.68 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 25.64 %
    Favored  : 70.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.27), residues: 1008
  helix:  2.06 (0.21), residues: 632
  sheet:  0.07 (0.69), residues: 55
  loop : -0.26 (0.38), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.012   0.001   TYR C 161 
 PHE   0.026   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.13 ( 8630)
  covalent geometry    : angle       0.47440 /  0.28 (12147)
  hydrogen bonds       : bond        0.04007 /  2.75 (  586)
  hydrogen bonds       : angle       4.36381 /  3.20 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   98 GLN cc_start: 0.6894 (tm-30) cc_final: 0.6395 (tp40)
  outliers start: 14
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0688
  time to fit residues: 10.9156
Evaluate side-chains
  117 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  108 MET
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  164 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:   30.0000
   chunk 95 optimal weight:    5.9990
   chunk 83 optimal weight:   40.0000
   chunk 7 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 73 optimal weight:   40.0000
   chunk 48 optimal weight:    4.9990
   chunk 27 optimal weight:   50.0000
   chunk 20 optimal weight:    0.2980
   chunk 53 optimal weight:    6.9990
   chunk 80 optimal weight:   20.0000
   overall best weight:    3.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 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 = 0.4155 r_free = 0.4155 target = 0.144615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.119603 restraints weight = 19524.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.117976 restraints weight = 27878.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.118879 restraints weight = 24438.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.118904 restraints weight = 16952.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.118859 restraints weight = 19436.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8630  Z= 0.250
  Angle     :  0.562   6.548  12147  Z= 0.318
  Chirality :  0.040   0.150   1532
  Planarity :  0.004   0.037   1306
  Dihedral  : 15.726 174.489   2335
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.68 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 25.13 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.27), residues: 1008
  helix:  1.91 (0.21), residues: 632
  sheet: -0.14 (0.69), residues: 57
  loop : -0.41 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 126 
 TYR   0.017   0.002   TYR C 161 
 PHE   0.032   0.003   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.005   0.002   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00540 /  0.25 ( 8630)
  covalent geometry    : angle       0.56167 /  0.32 (12147)
  hydrogen bonds       : bond        0.05099 /  3.51 (  586)
  hydrogen bonds       : angle       4.55588 /  3.33 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: B  730 LYS cc_start: 0.8439 (tttm) cc_final: 0.8219 (tttm)
REVERT: C   98 GLN cc_start: 0.6950 (tm-30) cc_final: 0.6464 (tp40)
REVERT: C  163 MET cc_start: 0.6431 (tpp) cc_final: 0.6130 (mmt)
  outliers start: 18
  outliers final: 15
  residues processed: 111
  average time/residue: 0.0689
  time to fit residues: 11.0217
Evaluate side-chains
  112 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 77 optimal weight:   20.0000
   chunk 14 optimal weight:    0.6980
   chunk 45 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 42 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   overall best weight:    2.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 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 = 0.4162 r_free = 0.4162 target = 0.145168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.119710 restraints weight = 19314.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.118451 restraints weight = 27670.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.119547 restraints weight = 24565.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.119411 restraints weight = 16696.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.119559 restraints weight = 16601.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8630  Z= 0.198
  Angle     :  0.519   6.445  12147  Z= 0.297
  Chirality :  0.039   0.156   1532
  Planarity :  0.003   0.037   1306
  Dihedral  : 15.804 174.906   2335
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.78 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 25.13 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.27), residues: 1008
  helix:  1.97 (0.21), residues: 632
  sheet: -0.14 (0.70), residues: 57
  loop : -0.41 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 126 
 TYR   0.013   0.002   TYR C 161 
 PHE   0.031   0.003   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00431 /  0.20 ( 8630)
  covalent geometry    : angle       0.51884 /  0.30 (12147)
  hydrogen bonds       : bond        0.04469 /  3.07 (  586)
  hydrogen bonds       : angle       4.44556 /  3.25 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   98 GLN cc_start: 0.7018 (tm-30) cc_final: 0.6744 (tm-30)
  outliers start: 15
  outliers final: 13
  residues processed: 111
  average time/residue: 0.0669
  time to fit residues: 10.5478
Evaluate side-chains
  112 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    8.9990
   chunk 92 optimal weight:   30.0000
   chunk 103 optimal weight:   10.0000
   chunk 88 optimal weight:   20.0000
   chunk 32 optimal weight:   50.0000
   chunk 94 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 76 optimal weight:   20.0000
   chunk 95 optimal weight:    3.9990
   chunk 71 optimal weight:    0.1980
   chunk 97 optimal weight:   10.0000
   overall best weight:    5.4388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 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 = 0.4126 r_free = 0.4126 target = 0.142669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.117580 restraints weight = 19507.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.115996 restraints weight = 32226.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.116677 restraints weight = 27282.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.116771 restraints weight = 20182.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.116967 restraints weight = 17983.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.3180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.077   8630  Z= 0.353
  Angle     :  0.677   7.528  12147  Z= 0.376
  Chirality :  0.044   0.181   1532
  Planarity :  0.004   0.045   1306
  Dihedral  : 15.953 177.979   2335
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.88 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 24.87 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.27), residues: 1008
  helix:  1.51 (0.20), residues: 632
  sheet: -0.09 (0.71), residues: 57
  loop : -0.63 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 744 
 TYR   0.023   0.002   TYR D 103 
 PHE   0.033   0.004   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.007   0.002   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00769 /  0.35 ( 8630)
  covalent geometry    : angle       0.67736 /  0.38 (12147)
  hydrogen bonds       : bond        0.06149 /  4.21 (  586)
  hydrogen bonds       : angle       4.86745 /  3.56 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.8139 (ppp) cc_final: 0.7625 (ptp)
REVERT: B  738 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7232 (mm-30)
REVERT: C   98 GLN cc_start: 0.7125 (tm-30) cc_final: 0.6808 (tm-30)
  outliers start: 19
  outliers final: 17
  residues processed: 105
  average time/residue: 0.0718
  time to fit residues: 10.8265
Evaluate side-chains
  111 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  734 THR
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain B residue  740 MET
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  137 SER
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 61 optimal weight:    0.2980
   chunk 48 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 28 optimal weight:   30.0000
   chunk 84 optimal weight:   40.0000
   chunk 67 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   overall best weight:    1.7986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.145915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.121959 restraints weight = 19475.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.120434 restraints weight = 33452.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.121292 restraints weight = 26152.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.121459 restraints weight = 19330.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.121306 restraints weight = 20888.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8630  Z= 0.152
  Angle     :  0.518   7.243  12147  Z= 0.296
  Chirality :  0.038   0.150   1532
  Planarity :  0.003   0.039   1306
  Dihedral  : 15.953 176.655   2335
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.58 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 26.67 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.27), residues: 1008
  helix:  1.88 (0.21), residues: 634
  sheet: -0.08 (0.71), residues: 57
  loop : -0.53 (0.37), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.018   0.001   TYR C 161 
 PHE   0.024   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS D 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.15 ( 8630)
  covalent geometry    : angle       0.51755 /  0.30 (12147)
  hydrogen bonds       : bond        0.04303 /  2.96 (  586)
  hydrogen bonds       : angle       4.46378 /  3.27 ( 1622)

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

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.8060 (ppp) cc_final: 0.7686 (ptp)
REVERT: B  738 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7153 (mm-30)
REVERT: C   98 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6777 (tm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0634
  time to fit residues: 9.9654
Evaluate side-chains
  111 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 ASP
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  143 GLU
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:   50.0000
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:   20.0000
   chunk 58 optimal weight:    0.7980
   chunk 104 optimal weight:   10.0000
   chunk 67 optimal weight:    0.8980
   chunk 5 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.1182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 721 GLN
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.146738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.122764 restraints weight = 19366.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.122646 restraints weight = 25279.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.122958 restraints weight = 20585.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.122657 restraints weight = 15049.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.122673 restraints weight = 15294.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8630  Z= 0.127
  Angle     :  0.488   9.705  12147  Z= 0.277
  Chirality :  0.037   0.159   1532
  Planarity :  0.003   0.042   1306
  Dihedral  : 15.824 176.165   2335
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.88 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 25.90 %
    Favored  : 70.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.27), residues: 1008
  helix:  2.10 (0.21), residues: 635
  sheet:  0.06 (0.72), residues: 57
  loop : -0.35 (0.38), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 736 
 TYR   0.020   0.001   TYR C 161 
 PHE   0.024   0.002   PHE C 144 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 ( 8630)
  covalent geometry    : angle       0.48800 /  0.28 (12147)
  hydrogen bonds       : bond        0.03922 /  2.70 (  586)
  hydrogen bonds       : angle       4.27106 /  3.14 ( 1622)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1077.73 seconds
wall clock time: 19 minutes 16.41 seconds (1156.41 seconds total)