Starting phenix.real_space_refine
on Wed Aug  5 04:11:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw1_54295/08_2026/9rw1_54295.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw1_54295/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw1_54295/08_2026/9rw1_54295.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw1_54295/08_2026/9rw1_54295.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw1_54295/08_2026/9rw1_54295.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw1_54295/08_2026/9rw1_54295.map"
  }
  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-2.2rc3-6140/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: 1.73, per 1000 atoms: 0.21
  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: 0.73
  Conformation dependent library (CDL) restraints added in 283.5 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: 1.29
  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: 1.59

  Time building geometry restraints manager: 0.92 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=" O3'   A E  32 "
       pdb=" P     C E  33 "
    ideal  model  delta    sigma   weight residual
    1.607  1.657 -0.050 1.20e-02 6.94e+03 1.71e+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=" 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 -     2.12: 11829
        2.12 -     4.24: 298
        4.24 -     6.35: 18
        6.35 -     8.47: 0
        8.47 -    10.59: 2
  Bond angle restraints: 12147
  Sorted by residual:
  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 1.60e+00 3.91e-01 4.38e+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
  angle pdb=" N6    A F  29 "
        pdb=" C6    A F  29 "
        pdb=" N1    A F  29 "
      ideal   model   delta    sigma   weight residual
     118.60  115.38    3.22 6.00e-01 2.78e+00 2.89e+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 -    0.074: 1336
       0.074 -    0.148: 183
       0.148 -    0.221: 11
       0.221 -    0.295: 1
       0.295 -    0.369: 1
  Chirality restraints: 1532
  Sorted by residual:
  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=" 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     -2.62   -2.34   -0.28 2.00e-01 2.50e+01 1.95e+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:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.290
  Find NCS groups from input model:        0.120
  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:   11.940
-------------------------------------------------------------------------------
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      :  0.004   0.103   8630  Z= 0.318
  Angle     :  0.738  10.588  12147  Z= 0.677
  Chirality :  0.049   0.369   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        0.00353 /  0.32 ( 8630)
  covalent geometry    : angle       0.73751 /  0.68 (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  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  728 GLN cc_start: 0.7544 (mt0) cc_final: 0.7341 (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: 0.4309 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 123
  average time/residue: 0.0798
  time to fit residues: 13.5932
Evaluate side-chains
  109 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
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 = 0.145129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.119871 restraints weight = 19622.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.118085 restraints weight = 30808.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.119093 restraints weight = 28838.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.118940 restraints weight = 17779.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.119146 restraints weight = 18334.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8630  Z= 0.263
  Angle     :  0.624   6.758  12147  Z= 0.351
  Chirality :  0.044   0.214   1532
  Planarity :  0.004   0.032   1306
  Dihedral  : 15.550 168.274   2337
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.78 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 18.97 %
    Favored  : 76.15 %
  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:  1.26 (0.27), residues: 1008
  helix:  1.61 (0.20), residues: 631
  sheet: -0.41 (0.63), residues: 55
  loop : -0.41 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 744 
 TYR   0.017   0.002   TYR C  64 
 PHE   0.024   0.003   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.002   HIS D  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00560 /  0.26 ( 8630)
  covalent geometry    : angle       0.62424 /  0.35 (12147)
  hydrogen bonds       : bond        0.05853 /  3.96 (  586)
  hydrogen bonds       : angle       5.16621 /  3.70 ( 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
  126 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: B  730 LYS cc_start: 0.8241 (tttm) cc_final: 0.7927 (tttm)
  outliers start: 19
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0606
  time to fit residues: 10.1691
Evaluate side-chains
  113 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
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:   40.0000
   chunk 106 optimal weight:   10.0000
   chunk 28 optimal weight:   40.0000
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.4196 r_free = 0.4196 target = 0.147864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.124188 restraints weight = 19551.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.122960 restraints weight = 29075.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.124113 restraints weight = 24345.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.123405 restraints weight = 17606.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.123644 restraints weight = 17221.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.1667

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= 0.131
  Angle     :  0.496   6.702  12147  Z= 0.287
  Chirality :  0.038   0.229   1532
  Planarity :  0.003   0.035   1306
  Dihedral  : 15.551 167.554   2335
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.18 %
    Favored  : 97.62 %
  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:  1.80 (0.27), residues: 1008
  helix:  2.05 (0.21), residues: 630
  sheet: -0.18 (0.63), residues: 55
  loop : -0.23 (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   0.023   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        0.00267 /  0.13 ( 8630)
  covalent geometry    : angle       0.49615 /  0.29 (12147)
  hydrogen bonds       : bond        0.04403 /  2.99 (  586)
  hydrogen bonds       : angle       4.65720 /  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
  129 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 12
  residues processed: 122
  average time/residue: 0.0658
  time to fit residues: 11.3088
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  : 0.172 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 31 optimal weight:    0.0010
   chunk 66 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   chunk 86 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 83 optimal weight:   50.0000
   chunk 20 optimal weight:    0.9990
   chunk 101 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.5592

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.147308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.122875 restraints weight = 19879.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.121663 restraints weight = 28754.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.122639 restraints weight = 23034.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.122470 restraints weight = 17037.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.122804 restraints weight = 16591.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.1974

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= 0.138
  Angle     :  0.484   6.314  12147  Z= 0.279
  Chirality :  0.038   0.213   1532
  Planarity :  0.003   0.043   1306
  Dihedral  : 15.477 169.495   2335
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.58 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 23.08 %
    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:  1.87 (0.27), residues: 1008
  helix:  2.10 (0.21), residues: 630
  sheet: -0.10 (0.64), residues: 55
  loop : -0.20 (0.38), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 744 
 TYR   0.010   0.001   TYR C  64 
 PHE   0.026   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        0.00288 /  0.14 ( 8630)
  covalent geometry    : angle       0.48440 /  0.28 (12147)
  hydrogen bonds       : bond        0.04301 /  2.93 (  586)
  hydrogen bonds       : angle       4.46380 /  3.24 ( 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
  122 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0722
  time to fit residues: 11.7813
Evaluate side-chains
  115 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
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   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:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 98 optimal weight:    0.0170
   chunk 44 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 27 optimal weight:   50.0000
   chunk 105 optimal weight:   20.0000
   chunk 56 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0020
   chunk 75 optimal weight:   50.0000
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.5428

-------------------------------------------------------------------------------
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 = 0.4208 r_free = 0.4208 target = 0.148835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.124029 restraints weight = 19748.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.122122 restraints weight = 29353.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.123257 restraints weight = 24635.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.122572 restraints weight = 16909.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.122974 restraints weight = 16718.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8630  Z= 0.106
  Angle     :  0.448   6.252  12147  Z= 0.259
  Chirality :  0.036   0.215   1532
  Planarity :  0.003   0.043   1306
  Dihedral  : 15.485 169.562   2335
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.38 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 23.85 %
    Favored  : 73.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.28), residues: 1008
  helix:  2.18 (0.20), residues: 636
  sheet:  0.12 (0.66), residues: 55
  loop : -0.03 (0.39), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 744 
 TYR   0.012   0.001   TYR C 161 
 PHE   0.017   0.002   PHE C  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.001   HIS D 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00205 /  0.11 ( 8630)
  covalent geometry    : angle       0.44774 /  0.26 (12147)
  hydrogen bonds       : bond        0.03705 /  2.51 (  586)
  hydrogen bonds       : angle       4.22815 /  3.09 ( 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
  123 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  736 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7109 (ttp80)
REVERT: D  160 ASP cc_start: 0.6576 (t70) cc_final: 0.6025 (t70)
REVERT: C  148 LEU cc_start: 0.6555 (mt) cc_final: 0.6341 (mt)
REVERT: C  149 MET cc_start: 0.5694 (mmt) cc_final: 0.5476 (tmm)
  outliers start: 9
  outliers final: 8
  residues processed: 118
  average time/residue: 0.0683
  time to fit residues: 11.4372
Evaluate side-chains
  109 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  123 LEU
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:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 42 optimal weight:   10.0000
   chunk 62 optimal weight:    0.3980
   chunk 50 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 32 optimal weight:   50.0000
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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 = 0.4203 r_free = 0.4203 target = 0.148449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.124045 restraints weight = 19595.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.122693 restraints weight = 28805.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.124261 restraints weight = 22612.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.123050 restraints weight = 17383.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.123818 restraints weight = 17145.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8630  Z= 0.113
  Angle     :  0.451   6.332  12147  Z= 0.260
  Chirality :  0.036   0.204   1532
  Planarity :  0.003   0.032   1306
  Dihedral  : 15.422 170.625   2335
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.28 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 24.62 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.27), residues: 1008
  helix:  2.27 (0.21), residues: 634
  sheet:  0.17 (0.67), residues: 55
  loop : -0.01 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 126 
 TYR   0.016   0.001   TYR C 161 
 PHE   0.016   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.001   HIS C 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.11 ( 8630)
  covalent geometry    : angle       0.45129 /  0.26 (12147)
  hydrogen bonds       : bond        0.03774 /  2.57 (  586)
  hydrogen bonds       : angle       4.14818 /  3.05 ( 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
  120 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: B  744 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.7192 (ttp80)
REVERT: D  160 ASP cc_start: 0.6645 (t70) cc_final: 0.6069 (t70)
REVERT: C  143 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6615 (mt-10)
REVERT: C  149 MET cc_start: 0.5683 (mmt) cc_final: 0.5458 (tmm)
  outliers start: 11
  outliers final: 10
  residues processed: 115
  average time/residue: 0.0637
  time to fit residues: 10.4824
Evaluate side-chains
  112 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  739 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  157 VAL
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
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:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 83 optimal weight:   50.0000
   chunk 7 optimal weight:    0.9990
   chunk 37 optimal weight:   30.0000
   chunk 73 optimal weight:   30.0000
   chunk 48 optimal weight:   10.0000
   chunk 27 optimal weight:   50.0000
   chunk 20 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0020
   chunk 80 optimal weight:   20.0000
   overall best weight:    1.9794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 106 ASN
** 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 = 0.4188 r_free = 0.4188 target = 0.147202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.123692 restraints weight = 19706.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.123582 restraints weight = 27326.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.124001 restraints weight = 21875.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.123421 restraints weight = 16739.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.123877 restraints weight = 15126.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8630  Z= 0.148
  Angle     :  0.486   6.443  12147  Z= 0.273
  Chirality :  0.038   0.195   1532
  Planarity :  0.003   0.032   1306
  Dihedral  : 15.416 171.838   2335
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.58 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 22.56 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.27), residues: 1008
  helix:  2.28 (0.20), residues: 633
  sheet:  0.25 (0.67), residues: 55
  loop :  0.00 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.020   0.001   TYR C 161 
 PHE   0.019   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        0.00315 /  0.15 ( 8630)
  covalent geometry    : angle       0.48598 /  0.27 (12147)
  hydrogen bonds       : bond        0.04057 /  2.77 (  586)
  hydrogen bonds       : angle       4.16528 /  3.06 ( 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
  121 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: B  736 ARG cc_start: 0.7385 (ttp80) cc_final: 0.7047 (ttp80)
REVERT: B  746 MET cc_start: 0.6548 (ttp) cc_final: 0.5693 (tpt)
REVERT: C  149 MET cc_start: 0.5940 (mmt) cc_final: 0.5695 (tmm)
  outliers start: 17
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0663
  time to fit residues: 10.7241
Evaluate side-chains
  116 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
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  106 ASN
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  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
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  164 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:   30.0000
   chunk 18 optimal weight:    2.9990
   chunk 77 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 28 optimal weight:   50.0000
   chunk 42 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 93 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   overall best weight:    3.6588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 106 ASN
** 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 = 0.4167 r_free = 0.4167 target = 0.145536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.120540 restraints weight = 19481.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.119441 restraints weight = 31363.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.120249 restraints weight = 25976.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.120422 restraints weight = 18394.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.120420 restraints weight = 19147.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8630  Z= 0.241
  Angle     :  0.566   6.550  12147  Z= 0.313
  Chirality :  0.042   0.185   1532
  Planarity :  0.004   0.032   1306
  Dihedral  : 15.481 173.302   2335
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.58 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 23.33 %
    Favored  : 72.05 %
  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:  1.94 (0.28), residues: 1008
  helix:  2.12 (0.21), residues: 635
  sheet:  0.28 (0.69), residues: 55
  loop : -0.19 (0.39), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.019   0.002   TYR C 161 
 PHE   0.033   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        0.00527 /  0.24 ( 8630)
  covalent geometry    : angle       0.56630 /  0.31 (12147)
  hydrogen bonds       : bond        0.04846 /  3.30 (  586)
  hydrogen bonds       : angle       4.33518 /  3.19 ( 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: 18
    poor density    : 100
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: C  149 MET cc_start: 0.5786 (mmt) cc_final: 0.5548 (tmm)
REVERT: C  163 MET cc_start: 0.6201 (mmt) cc_final: 0.5733 (mmm)
  outliers start: 18
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0656
  time to fit residues: 10.3584
Evaluate side-chains
  114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
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  106 ASN
Chi-restraints excluded: chain D residue  157 VAL
Chi-restraints excluded: chain D residue  784 ILE
Chi-restraints excluded: chain D residue  813 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  127 SER
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  164 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    7.9990
   chunk 92 optimal weight:   50.0000
   chunk 103 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 32 optimal weight:   50.0000
   chunk 94 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 76 optimal weight:   20.0000
   chunk 95 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    6.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 GLN
C  98 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.142534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.117373 restraints weight = 19542.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.115593 restraints weight = 28799.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.116344 restraints weight = 26310.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.116407 restraints weight = 18924.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.116272 restraints weight = 21125.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.079   8630  Z= 0.371
  Angle     :  0.748   8.575  12147  Z= 0.400
  Chirality :  0.049   0.278   1532
  Planarity :  0.005   0.043   1306
  Dihedral  : 15.859 176.949   2335
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.88 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 24.87 %
    Favored  : 70.00 %
  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:  1.01 (0.27), residues: 1008
  helix:  1.45 (0.20), residues: 631
  sheet: -0.10 (0.71), residues: 57
  loop : -0.67 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 126 
 TYR   0.032   0.003   TYR D 103 
 PHE   0.038   0.005   PHE C 144 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.015   0.003   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00804 /  0.37 ( 8630)
  covalent geometry    : angle       0.74806 /  0.40 (12147)
  hydrogen bonds       : bond        0.06557 /  4.49 (  586)
  hydrogen bonds       : angle       4.93992 /  3.62 ( 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
  120 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: B  738 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7312 (mm-30)
REVERT: C   26 GLU cc_start: 0.8336 (pm20) cc_final: 0.8105 (mp0)
  outliers start: 20
  outliers final: 15
  residues processed: 112
  average time/residue: 0.0576
  time to fit residues: 9.1679
Evaluate side-chains
  110 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
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 D residue   29 THR
Chi-restraints excluded: chain D residue  106 ASN
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
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 84 optimal weight:   40.0000
   chunk 67 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 = 0.4157 r_free = 0.4157 target = 0.144891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.120010 restraints weight = 19504.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.119293 restraints weight = 28711.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.120102 restraints weight = 25600.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.120130 restraints weight = 17398.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.120282 restraints weight = 17640.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8630  Z= 0.206
  Angle     :  0.576   6.843  12147  Z= 0.320
  Chirality :  0.041   0.210   1532
  Planarity :  0.003   0.033   1306
  Dihedral  : 15.823 175.107   2335
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.68 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 24.87 %
    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:  1.46 (0.27), residues: 1008
  helix:  1.81 (0.20), residues: 636
  sheet: -0.01 (0.71), residues: 57
  loop : -0.53 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 736 
 TYR   0.017   0.002   TYR C 161 
 PHE   0.026   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        0.00454 /  0.21 ( 8630)
  covalent geometry    : angle       0.57640 /  0.32 (12147)
  hydrogen bonds       : bond        0.04817 /  3.32 (  586)
  hydrogen bonds       : angle       4.54776 /  3.34 ( 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
  120 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: B  738 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7173 (mm-30)
REVERT: B  746 MET cc_start: 0.6564 (ttp) cc_final: 0.5774 (tpt)
REVERT: C   98 GLN cc_start: 0.7194 (tm-30) cc_final: 0.6472 (tp40)
  outliers start: 17
  outliers final: 15
  residues processed: 111
  average time/residue: 0.0673
  time to fit residues: 10.6604
Evaluate side-chains
  114 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
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  106 ASN
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  108 MET
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  137 SER
Chi-restraints excluded: chain C residue  154 THR
Chi-restraints excluded: chain C residue  157 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 84 optimal weight:   40.0000
   chunk 58 optimal weight:    0.9980
   chunk 104 optimal weight:   20.0000
   chunk 67 optimal weight:    4.9990
   chunk 5 optimal weight:   20.0000
   chunk 93 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   overall best weight:    3.1988

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.144437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.119497 restraints weight = 19360.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.118268 restraints weight = 26535.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.119466 restraints weight = 23632.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.118799 restraints weight = 17293.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.119223 restraints weight = 19930.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8630  Z= 0.220
  Angle     :  0.586   8.806  12147  Z= 0.323
  Chirality :  0.041   0.194   1532
  Planarity :  0.003   0.039   1306
  Dihedral  : 15.801 175.925   2335
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.17 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 26.15 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.51 (0.27), residues: 1008
  helix:  1.82 (0.20), residues: 636
  sheet:  0.01 (0.72), residues: 57
  loop : -0.45 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.018   0.002   TYR C 161 
 PHE   0.027   0.003   PHE C 144 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.005   0.001   HIS C 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00484 /  0.22 ( 8630)
  covalent geometry    : angle       0.58617 /  0.32 (12147)
  hydrogen bonds       : bond        0.04930 /  3.40 (  586)
  hydrogen bonds       : angle       4.52651 /  3.32 ( 1622)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 991.61 seconds
wall clock time: 17 minutes 48.27 seconds (1068.27 seconds total)