Starting phenix.real_space_refine
on Wed Aug  5 02:50:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw2_54296/08_2026/9rw2_54296.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw2_54296/08_2026/9rw2_54296.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rw2_54296/08_2026/9rw2_54296.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw2_54296/08_2026/9rw2_54296.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw2_54296/08_2026/9rw2_54296.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw2_54296/08_2026/9rw2_54296.cif"
  }
  resolution = 3.6
  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      19      5.16       5
     C    4693      2.51       5
     N    1490      2.21       5
     O    1837      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  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: 8127
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 365
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 58
    Chain: "B"
      Number of atoms: 365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 365
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'TRANS': 52}
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 98
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 58
    Chain: "D"
      Number of atoms: 2780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 462, 2780
          Classifications: {'peptide': 462}
          Incomplete info: {'truncation_to_alanine': 274}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450}
          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: "C"
      Number of atoms: 2767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 460, 2767
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 274}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448}
          Chain breaks: 3
          Unresolved chain link angles: 7
          Unresolved non-hydrogen bonds: 981
          Unresolved non-hydrogen angles: 1242
          Unresolved non-hydrogen dihedrals: 801
          Unresolved non-hydrogen chiralities: 94
          Planarities with less than four sites: {'GLU:plan': 22, 'ASN:plan1': 17, 'TYR:plan': 12, 'ASP:plan': 16, 'TRP:plan': 2, 'GLN:plan1': 20, 'PHE:plan': 8, 'ARG:plan': 15, 'HIS:plan': 4}
          Unresolved non-hydrogen planarities: 512
    Chain: "E"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
    Chain: "F"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 925
          Classifications: {'RNA': 44}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 21, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 1, 'rna3p': 42}
  Time building chain proxies: 2.00, per 1000 atoms: 0.25
  Number of scatterers: 8127
  At special positions: 0
  Unit cell: (94.251, 95.31, 175.794, 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      19     16.00
     P      88     15.00
     O    1837      8.00
     N    1490      7.00
     C    4693      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: 0.87
  Conformation dependent library (CDL) restraints added in 298.2 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
      68.6% alpha, 5.7% beta
      34 base pairs and 54 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 695 through 747
      removed outlier: 3.605A  pdb=" N   VAL A 699 " --> pdb=" O   CYS A 695 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 696 through 747
    Processing helix  chain 'D' and resid 3 through 25
      removed outlier: 3.672A  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
      removed outlier: 3.542A  pdb=" N   GLN D  63 " --> pdb=" O   LYS D  59 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 110
    Processing helix  chain 'D' and resid 119 through 125
      removed outlier: 3.865A  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 530
    Processing helix  chain 'D' and resid 535 through 554
    Processing helix  chain 'D' and resid 594 through 600
      removed outlier: 3.940A  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 617 through 628
      removed outlier: 4.540A  pdb=" N   ASP D 621 " --> pdb=" O   ASP D 617 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 639 through 652
    Processing helix  chain 'D' and resid 654 through 658
    Processing helix  chain 'D' and resid 662 through 670
      removed outlier: 3.642A  pdb=" N   TYR D 670 " --> pdb=" O   LEU D 666 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 676 through 680
    Processing helix  chain 'D' and resid 681 through 688
      removed outlier: 3.817A  pdb=" N   TYR D 685 " --> pdb=" O   LEU D 681 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 714
      removed outlier: 3.546A  pdb=" N   MET D 702 " --> pdb=" O   THR D 698 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL D 709 " --> pdb=" O   ALA D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 717 through 725
    Processing helix  chain 'D' and resid 726 through 728
      No H-bonds generated for 'chain 'D' and resid 726 through 728'
    Processing helix  chain 'D' and resid 729 through 743
    Processing helix  chain 'D' and resid 746 through 773
      removed outlier: 3.894A  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 802
      removed outlier: 4.014A  pdb=" N   GLY D 802 " --> pdb=" O   GLU D 798 " (cutoff:3.500A)
    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 50
      removed outlier: 3.950A  pdb=" N   MET C  46 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 53 through 62
    Processing helix  chain 'C' and resid 96 through 110
      removed outlier: 3.687A  pdb=" N   GLN C 110 " --> pdb=" O   ASN C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 127
    Processing helix  chain 'C' and resid 130 through 138
      removed outlier: 3.569A  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
      removed outlier: 3.642A  pdb=" N   GLN C 528 " --> pdb=" O   ILE C 524 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ASN C 529 " --> pdb=" O   LYS C 525 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 535 through 554
    Processing helix  chain 'C' and resid 594 through 600
      removed outlier: 3.879A  pdb=" N   THR C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 601 through 608
      removed outlier: 3.629A  pdb=" N   VAL C 605 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 617 through 629
      removed outlier: 4.366A  pdb=" N   ASP C 621 " --> pdb=" O   ASP C 617 " (cutoff:3.500A)
    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: 3.625A  pdb=" N   TYR C 670 " --> pdb=" O   LEU C 666 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 675 through 680
      removed outlier: 3.867A  pdb=" N   LYS C 678 " --> pdb=" O   ASN C 675 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 681 through 688
      removed outlier: 4.433A  pdb=" N   TYR C 685 " --> pdb=" O   LEU C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 698 through 714
      removed outlier: 3.695A  pdb=" N   MET C 702 " --> pdb=" O   THR C 698 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASP C 708 " --> pdb=" O   TYR C 704 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   VAL C 709 " --> pdb=" O   ALA C 705 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   HIS C 714 " --> pdb=" O   LEU C 710 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 717 through 724
    Processing helix  chain 'C' and resid 729 through 743
    Processing helix  chain 'C' and resid 746 through 773
      removed outlier: 4.140A  pdb=" N   THR C 773 " --> pdb=" O   LYS C 769 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 780 through 787
      removed outlier: 3.808A  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 800
    Processing helix  chain 'C' and resid 803 through 816
      removed outlier: 3.653A  pdb=" N   GLU C 814 " --> pdb=" O   LEU C 810 " (cutoff:3.500A)
    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 531 through 533
      removed outlier: 3.501A  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 155 through 158
    Processing sheet with id=AA6, first strand: chain 'C' and resid 585 through 588
      removed outlier: 3.544A  pdb=" N   ILE C 578 " --> pdb=" O   PHE C 586 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE C 576 " --> pdb=" O   PHE C 588 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   LYS C 613 " --> pdb=" O   PHE C 637 " (cutoff:3.500A)

    498 hydrogen bonds defined for protein.
    1440 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      72 hydrogen bonds
      136 hydrogen bond angles
      0 basepair planarities
      34 basepair parallelities
      54 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1710
        1.33 -     1.45: 2184
        1.45 -     1.57: 4286
        1.57 -     1.69: 174
        1.69 -     1.82: 34
  Bond restraints: 8388
  Sorted by residual:
  bond pdb=" N1    C F   1 "
       pdb=" C6    C F   1 "
    ideal  model  delta    sigma   weight residual
    1.367  1.383 -0.016 6.00e-03 2.78e+04 7.17e+00
  bond pdb=" C5'   U F   2 "
       pdb=" C4'   U F   2 "
    ideal  model  delta    sigma   weight residual
    1.508  1.525 -0.017 7.00e-03 2.04e+04 6.01e+00
  bond pdb=" N1    C F  36 "
       pdb=" C6    C F  36 "
    ideal  model  delta    sigma   weight residual
    1.367  1.381 -0.014 6.00e-03 2.78e+04 5.57e+00
  bond pdb=" N9    A F  37 "
       pdb=" C4    A F  37 "
    ideal  model  delta    sigma   weight residual
    1.374  1.387 -0.013 6.00e-03 2.78e+04 5.00e+00
  bond pdb=" N1    U F  11 "
       pdb=" C6    U F  11 "
    ideal  model  delta    sigma   weight residual
    1.375  1.395 -0.020 9.00e-03 1.23e+04 4.97e+00
  ... (remaining 8383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 10931
        1.29 -     2.58: 791
        2.58 -     3.86: 102
        3.86 -     5.15: 18
        5.15 -     6.44: 7
  Bond angle restraints: 11849
  Sorted by residual:
  angle pdb=" N6    A F  37 "
        pdb=" C6    A F  37 "
        pdb=" N1    A F  37 "
      ideal   model   delta    sigma   weight residual
     118.60  115.03    3.57 6.00e-01 2.78e+00 3.55e+01
  angle pdb=" N6    A F  22 "
        pdb=" C6    A F  22 "
        pdb=" N1    A F  22 "
      ideal   model   delta    sigma   weight residual
     118.60  115.56    3.04 6.00e-01 2.78e+00 2.57e+01
  angle pdb=" N6    A F  21 "
        pdb=" C6    A F  21 "
        pdb=" N1    A F  21 "
      ideal   model   delta    sigma   weight residual
     118.60  115.59    3.01 6.00e-01 2.78e+00 2.51e+01
  angle pdb=" C1'   U E  11 "
        pdb=" N1    U E  11 "
        pdb=" C2    U E  11 "
      ideal   model   delta    sigma   weight residual
     117.70  123.60   -5.90 1.20e+00 6.94e-01 2.42e+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  115.65    2.95 6.00e-01 2.78e+00 2.42e+01
  ... (remaining 11844 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.89: 4865
       35.89 -    71.78: 179
       71.78 -   107.67: 15
      107.67 -   143.57: 0
      143.57 -   179.46: 2
  Dihedral angle restraints: 5061
    sinusoidal: 2063
      harmonic: 2998
  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   40.54  179.46     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   45.91  174.09     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  THR D 574 "
           pdb=" C   THR D 574 "
           pdb=" N   LEU D 575 "
           pdb=" CA  LEU D 575 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.66   18.34     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 5058 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1066
       0.038 -    0.077: 270
       0.077 -    0.115: 141
       0.115 -    0.153: 30
       0.153 -    0.192: 9
  Chirality restraints: 1516
  Sorted by residual:
  chirality pdb=" C2'   C F  36 "
            pdb=" C3'   C F  36 "
            pdb=" O2'   C F  36 "
            pdb=" C1'   C F  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.81    0.19 2.00e-01 2.50e+01 9.18e-01
  chirality pdb=" C2'   A F  38 "
            pdb=" C3'   A F  38 "
            pdb=" O2'   A F  38 "
            pdb=" C1'   A F  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.79    0.18 2.00e-01 2.50e+01 7.67e-01
  chirality pdb=" C3'   A F  32 "
            pdb=" C4'   A F  32 "
            pdb=" O3'   A F  32 "
            pdb=" C2'   A F  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.65    0.17 2.00e-01 2.50e+01 7.47e-01
  ... (remaining 1513 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  21 "   -0.051 2.00e-02 2.50e+03   2.17e-02 1.29e+01
        pdb=" N9    A F  21 "    0.017 2.00e-02 2.50e+03
        pdb=" C8    A F  21 "    0.009 2.00e-02 2.50e+03
        pdb=" N7    A F  21 "    0.012 2.00e-02 2.50e+03
        pdb=" C5    A F  21 "    0.012 2.00e-02 2.50e+03
        pdb=" C6    A F  21 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A F  21 "   -0.037 2.00e-02 2.50e+03
        pdb=" N1    A F  21 "   -0.006 2.00e-02 2.50e+03
        pdb=" C2    A F  21 "    0.006 2.00e-02 2.50e+03
        pdb=" N3    A F  21 "    0.016 2.00e-02 2.50e+03
        pdb=" C4    A F  21 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A F  10 "   -0.052 2.00e-02 2.50e+03   2.16e-02 1.28e+01
        pdb=" N9    A F  10 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    A F  10 "    0.016 2.00e-02 2.50e+03
        pdb=" N7    A F  10 "    0.010 2.00e-02 2.50e+03
        pdb=" C5    A F  10 "    0.003 2.00e-02 2.50e+03
        pdb=" C6    A F  10 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6    A F  10 "   -0.032 2.00e-02 2.50e+03
        pdb=" N1    A F  10 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A F  10 "    0.007 2.00e-02 2.50e+03
        pdb=" N3    A F  10 "    0.012 2.00e-02 2.50e+03
        pdb=" C4    A F  10 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G F   8 "   -0.046 2.00e-02 2.50e+03   1.96e-02 1.15e+01
        pdb=" N9    G F   8 "    0.019 2.00e-02 2.50e+03
        pdb=" C8    G F   8 "    0.025 2.00e-02 2.50e+03
        pdb=" N7    G F   8 "    0.016 2.00e-02 2.50e+03
        pdb=" C5    G F   8 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G F   8 "   -0.011 2.00e-02 2.50e+03
        pdb=" O6    G F   8 "   -0.021 2.00e-02 2.50e+03
        pdb=" N1    G F   8 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2    G F   8 "   -0.005 2.00e-02 2.50e+03
        pdb=" N2    G F   8 "    0.024 2.00e-02 2.50e+03
        pdb=" N3    G F   8 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G F   8 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 56
        2.57 -     3.15: 7026
        3.15 -     3.74: 13440
        3.74 -     4.32: 16517
        4.32 -     4.90: 25564
  Nonbonded interactions: 62603
  Sorted by model distance:
  nonbonded pdb=" O2'   C E  33 "
            pdb=" OP1   U E  34 "
     model   vdw
     1.990 3.040
  nonbonded pdb=" OG1 THR D  43 "
            pdb=" OE1 GLU D  45 "
     model   vdw
     2.005 3.040
  nonbonded pdb=" NE2 GLN C 139 "
            pdb=" OP1   A F  30 "
     model   vdw
     2.070 3.120
  nonbonded pdb=" O2'   C E  36 "
            pdb=" OP1   A E  38 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OG  SER C  55 "
            pdb=" NZ  LYS C  59 "
     model   vdw
     2.189 3.120
  ... (remaining 62598 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 816)
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.710
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8388  Z= 0.282
  Angle     :  0.709   6.438  11849  Z= 0.646
  Chirality :  0.046   0.192   1516
  Planarity :  0.004   0.056   1272
  Dihedral  : 17.557 179.458   3097
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 21.30 %
    Favored  : 78.70 %
  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:  0.32 (0.26), residues: 1008
  helix:  0.86 (0.20), residues: 609
  sheet: -1.78 (0.62), residues: 61
  loop : -0.41 (0.36), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG C 126 
 TYR   0.013   0.001   TYR D   6 
 PHE   0.009   0.001   PHE C  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.28 ( 8388)
  covalent geometry    : angle       0.70929 /  0.65 (11849)
  hydrogen bonds       : bond        0.15592 / 11.02 (  570)
  hydrogen bonds       : angle       6.50985 /  4.81 ( 1576)

*********************** 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
  111 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.169 
Fit side-chains
REVERT: B  714 GLU cc_start: 0.7777 (tp30) cc_final: 0.7503 (tp30)
REVERT: B  716 LYS cc_start: 0.8351 (mttt) cc_final: 0.8119 (mttm)
REVERT: B  725 LEU cc_start: 0.8371 (mt) cc_final: 0.7632 (tp)
REVERT: D  160 ASP cc_start: 0.7684 (t70) cc_final: 0.7453 (t0)
REVERT: C   99 GLU cc_start: 0.8471 (tt0) cc_final: 0.7802 (tt0)
REVERT: C  102 ASP cc_start: 0.8471 (m-30) cc_final: 0.8122 (p0)
REVERT: C  111 TYR cc_start: 0.6881 (m-10) cc_final: 0.6443 (m-10)
REVERT: C  126 ARG cc_start: 0.7594 (tmt170) cc_final: 0.6791 (tmm-80)
REVERT: C  146 ASP cc_start: 0.8590 (m-30) cc_final: 0.8320 (m-30)
REVERT: C  149 MET cc_start: 0.8167 (mtp) cc_final: 0.7936 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0764
  time to fit residues: 11.6677
Evaluate side-chains
  95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:   30.0000
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:   40.0000
   chunk 33 optimal weight:    0.0170
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:   30.0000
   chunk 106 optimal weight:    9.9990
   overall best weight:    6.3024

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 128 GLN
C 132 GLN
** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.103727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.082042 restraints weight = 32180.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.081850 restraints weight = 24447.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.082959 restraints weight = 18248.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.083040 restraints weight = 15236.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.083050 restraints weight = 13657.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062   8388  Z= 0.335
  Angle     :  0.704   8.423  11849  Z= 0.397
  Chirality :  0.046   0.233   1516
  Planarity :  0.005   0.046   1272
  Dihedral  : 15.964 163.514   2324
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.67 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  6.79 %
    Allowed  : 21.91 %
    Favored  : 71.30 %
  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:  0.48 (0.26), residues: 1008
  helix:  1.00 (0.19), residues: 648
  sheet: -1.69 (0.64), residues: 59
  loop : -0.58 (0.37), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 126 
 TYR   0.016   0.002   TYR C  64 
 PHE   0.025   0.003   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.007   0.002   HIS D 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00687 /  0.33 ( 8388)
  covalent geometry    : angle       0.70387 /  0.40 (11849)
  hydrogen bonds       : bond        0.06533 /  4.56 (  570)
  hydrogen bonds       : angle       5.22917 /  3.96 ( 1576)

*********************** 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
  115 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  714 GLU cc_start: 0.8040 (tp30) cc_final: 0.7798 (tp30)
REVERT: B  716 LYS cc_start: 0.8456 (mttt) cc_final: 0.7987 (mttm)
REVERT: D  108 MET cc_start: 0.8528 (mmm) cc_final: 0.8155 (mmm)
REVERT: C   99 GLU cc_start: 0.8357 (tt0) cc_final: 0.7694 (tt0)
REVERT: C  116 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7623 (mm-30)
REVERT: C  123 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8051 (mm)
REVERT: C  126 ARG cc_start: 0.7747 (tmt170) cc_final: 0.6944 (tmm-80)
  outliers start: 22
  outliers final: 15
  residues processed: 109
  average time/residue: 0.0689
  time to fit residues: 10.4191
Evaluate side-chains
  100 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  728 GLN
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue   13 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  145 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 75 optimal weight:   40.0000
   chunk 49 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:   40.0000
   chunk 4 optimal weight:    3.9990
   chunk 47 optimal weight:   30.0000
   chunk 59 optimal weight:    0.9980
   chunk 106 optimal weight:   10.0000
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  54 GLN
** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 110 GLN
C 139 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.105701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.084814 restraints weight = 31956.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.083889 restraints weight = 24126.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.085264 restraints weight = 18757.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.085550 restraints weight = 14505.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.085495 restraints weight = 13165.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   8388  Z= 0.157
  Angle     :  0.516   6.101  11849  Z= 0.298
  Chirality :  0.038   0.186   1516
  Planarity :  0.003   0.036   1272
  Dihedral  : 15.978 165.333   2324
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.08 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 23.15 %
    Favored  : 72.22 %
  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:  1.49 (0.27), residues: 1008
  helix:  1.83 (0.20), residues: 649
  sheet: -1.55 (0.62), residues: 57
  loop : -0.27 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 126 
 TYR   0.012   0.002   TYR C  64 
 PHE   0.017   0.002   PHE C 104 
 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        0.00330 /  0.16 ( 8388)
  covalent geometry    : angle       0.51593 /  0.30 (11849)
  hydrogen bonds       : bond        0.04630 /  3.17 (  570)
  hydrogen bonds       : angle       4.57778 /  3.47 ( 1576)

*********************** 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
  112 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8226 (mmmt)
REVERT: B  716 LYS cc_start: 0.8506 (mttt) cc_final: 0.8045 (mttm)
REVERT: D  108 MET cc_start: 0.8300 (mmm) cc_final: 0.8030 (mmm)
REVERT: C   73 ASP cc_start: 0.8085 (p0) cc_final: 0.7856 (p0)
REVERT: C   98 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8297 (tm-30)
REVERT: C  102 ASP cc_start: 0.7661 (p0) cc_final: 0.7311 (p0)
REVERT: C  123 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7755 (mm)
REVERT: C  126 ARG cc_start: 0.7672 (tmt170) cc_final: 0.6794 (tmm-80)
  outliers start: 15
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0900
  time to fit residues: 13.5300
Evaluate side-chains
  96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  152 THR
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  110 GLN
Chi-restraints excluded: chain C residue  117 VAL
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 67 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 95 optimal weight:   20.0000
   chunk 82 optimal weight:   30.0000
   chunk 48 optimal weight:   20.0000
   chunk 104 optimal weight:   30.0000
   chunk 4 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    9.9990
   chunk 58 optimal weight:    0.0270
   overall best weight:    2.5644

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 110 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.102865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.081355 restraints weight = 31119.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.080869 restraints weight = 20748.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.082219 restraints weight = 17091.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.082417 restraints weight = 13195.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.082334 restraints weight = 11707.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8388  Z= 0.167
  Angle     :  0.516   8.246  11849  Z= 0.294
  Chirality :  0.039   0.215   1516
  Planarity :  0.003   0.035   1272
  Dihedral  : 15.936 163.469   2324
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.37 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 22.22 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.27), residues: 1008
  helix:  2.01 (0.20), residues: 647
  sheet: -1.14 (0.60), residues: 55
  loop : -0.09 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 126 
 TYR   0.013   0.002   TYR C  64 
 PHE   0.017   0.002   PHE C  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.17 ( 8388)
  covalent geometry    : angle       0.51569 /  0.29 (11849)
  hydrogen bonds       : bond        0.04506 /  3.09 (  570)
  hydrogen bonds       : angle       4.38095 /  3.32 ( 1576)

*********************** 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
  112 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8762 (mmmt) cc_final: 0.8304 (mmmt)
REVERT: B  716 LYS cc_start: 0.8536 (mttt) cc_final: 0.7994 (mttm)
REVERT: C  116 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7519 (mm-30)
REVERT: C  123 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7911 (mm)
REVERT: C  126 ARG cc_start: 0.7813 (tmt170) cc_final: 0.6880 (tmm-80)
  outliers start: 20
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0784
  time to fit residues: 11.9374
Evaluate side-chains
  98 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 90 optimal weight:   40.0000
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:   30.0000
   chunk 93 optimal weight:   30.0000
   chunk 11 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 42 optimal weight:   50.0000
   chunk 89 optimal weight:   20.0000
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.5788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.105221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.085595 restraints weight = 32465.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.084255 restraints weight = 26639.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.085673 restraints weight = 20367.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.085551 restraints weight = 16169.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.085585 restraints weight = 14071.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8388  Z= 0.164
  Angle     :  0.525   8.532  11849  Z= 0.298
  Chirality :  0.038   0.187   1516
  Planarity :  0.003   0.035   1272
  Dihedral  : 15.974 163.485   2324
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.98 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 24.07 %
    Favored  : 70.68 %
  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:  1.85 (0.27), residues: 1008
  helix:  2.04 (0.21), residues: 650
  sheet: -1.10 (0.58), residues: 55
  loop : -0.04 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  47 
 TYR   0.016   0.002   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 C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.16 ( 8388)
  covalent geometry    : angle       0.52454 /  0.30 (11849)
  hydrogen bonds       : bond        0.04380 /  2.99 (  570)
  hydrogen bonds       : angle       4.28624 /  3.25 ( 1576)

*********************** 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
  109 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8434 (mmmt)
REVERT: B  716 LYS cc_start: 0.8532 (mttt) cc_final: 0.7991 (mttm)
REVERT: B  736 ARG cc_start: 0.8995 (tmm-80) cc_final: 0.8764 (tpt-90)
REVERT: D   80 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7273 (m-80)
REVERT: C   73 ASP cc_start: 0.8197 (p0) cc_final: 0.7796 (p0)
REVERT: C  123 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7766 (mm)
REVERT: C  163 MET cc_start: 0.5435 (mtm) cc_final: 0.5033 (mmm)
  outliers start: 17
  outliers final: 11
  residues processed: 106
  average time/residue: 0.0843
  time to fit residues: 12.6690
Evaluate side-chains
  100 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   80 TYR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  165 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:   40.0000
   chunk 44 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 79 optimal weight:   30.0000
   chunk 63 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 37 optimal weight:   30.0000
   chunk 25 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 128 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.106176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.085525 restraints weight = 31963.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.084886 restraints weight = 24539.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.086234 restraints weight = 18265.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.086463 restraints weight = 14384.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.086407 restraints weight = 13207.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.057   8388  Z= 0.119
  Angle     :  0.494   8.310  11849  Z= 0.279
  Chirality :  0.037   0.181   1516
  Planarity :  0.003   0.036   1272
  Dihedral  : 15.983 163.070   2324
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.68 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 25.93 %
    Favored  : 70.68 %
  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:  2.05 (0.28), residues: 1008
  helix:  2.17 (0.21), residues: 645
  sheet: -1.01 (0.59), residues: 55
  loop :  0.13 (0.39), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  47 
 TYR   0.017   0.002   TYR C  96 
 PHE   0.016   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.001   HIS D 125 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.12 ( 8388)
  covalent geometry    : angle       0.49404 /  0.28 (11849)
  hydrogen bonds       : bond        0.03987 /  2.72 (  570)
  hydrogen bonds       : angle       4.10824 /  3.12 ( 1576)

*********************** 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
  104 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.285 
Fit side-chains
REVERT: B  716 LYS cc_start: 0.8496 (mttt) cc_final: 0.8019 (mttp)
REVERT: B  736 ARG cc_start: 0.8990 (tmm-80) cc_final: 0.8639 (tpt-90)
REVERT: C   73 ASP cc_start: 0.8085 (p0) cc_final: 0.7714 (p0)
REVERT: C   96 TYR cc_start: 0.7751 (m-80) cc_final: 0.7542 (m-80)
REVERT: C  123 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7648 (mm)
  outliers start: 11
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0903
  time to fit residues: 12.6346
Evaluate side-chains
  99 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain B residue  735 GLN
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0020
   chunk 1 optimal weight:    9.9990
   chunk 82 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0770
   chunk 104 optimal weight:   30.0000
   chunk 88 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.0152

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.104217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.082552 restraints weight = 30882.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.082617 restraints weight = 20108.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.083539 restraints weight = 14495.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.083910 restraints weight = 12133.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.083889 restraints weight = 10751.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.063   8388  Z= 0.112
  Angle     :  0.488   7.804  11849  Z= 0.275
  Chirality :  0.036   0.174   1516
  Planarity :  0.003   0.038   1272
  Dihedral  : 15.951 163.173   2324
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.79 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 26.23 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.22 (0.28), residues: 1008
  helix:  2.30 (0.21), residues: 645
  sheet: -0.95 (0.59), residues: 55
  loop :  0.21 (0.39), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 126 
 TYR   0.014   0.001   TYR C 103 
 PHE   0.021   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.001   0.000   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.11 ( 8388)
  covalent geometry    : angle       0.48790 /  0.27 (11849)
  hydrogen bonds       : bond        0.03775 /  2.58 (  570)
  hydrogen bonds       : angle       3.98319 /  3.03 ( 1576)

*********************** 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
  113 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  716 LYS cc_start: 0.8530 (mttt) cc_final: 0.8042 (mttm)
REVERT: B  736 ARG cc_start: 0.9011 (tmm-80) cc_final: 0.8590 (tpt-90)
REVERT: B  739 GLU cc_start: 0.8360 (pp20) cc_final: 0.7678 (pp20)
REVERT: B  740 MET cc_start: 0.8149 (ppp) cc_final: 0.7924 (ppp)
REVERT: D   39 ASN cc_start: 0.8461 (t0) cc_final: 0.8125 (t0)
REVERT: C   63 GLN cc_start: 0.7729 (mt0) cc_final: 0.7463 (tt0)
REVERT: C   73 ASP cc_start: 0.8180 (p0) cc_final: 0.7839 (p0)
REVERT: C   96 TYR cc_start: 0.7765 (m-80) cc_final: 0.7527 (m-80)
REVERT: C  123 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7655 (mm)
  outliers start: 12
  outliers final: 10
  residues processed: 110
  average time/residue: 0.0837
  time to fit residues: 12.8666
Evaluate side-chains
  101 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  728 GLN
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 83 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   chunk 55 optimal weight:   30.0000
   chunk 88 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 68 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 70 optimal weight:    0.6980
   chunk 99 optimal weight:   30.0000
   chunk 53 optimal weight:   20.0000
   overall best weight:    3.3388

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.104556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.085227 restraints weight = 32236.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.085447 restraints weight = 22311.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.086107 restraints weight = 18276.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.085730 restraints weight = 14763.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.085958 restraints weight = 15813.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8388  Z= 0.191
  Angle     :  0.567   7.890  11849  Z= 0.313
  Chirality :  0.039   0.184   1516
  Planarity :  0.004   0.038   1272
  Dihedral  : 15.973 163.438   2324
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.88 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 26.54 %
    Favored  : 68.83 %
  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 (0.28), residues: 1008
  helix:  2.21 (0.21), residues: 645
  sheet: -0.78 (0.62), residues: 55
  loop :  0.27 (0.38), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  47 
 TYR   0.016   0.002   TYR C 161 
 PHE   0.017   0.003   PHE C  60 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.19 ( 8388)
  covalent geometry    : angle       0.56669 /  0.31 (11849)
  hydrogen bonds       : bond        0.04412 /  3.02 (  570)
  hydrogen bonds       : angle       4.08859 /  3.10 ( 1576)

*********************** 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
  107 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.309 
Fit side-chains
REVERT: B  716 LYS cc_start: 0.8544 (mttt) cc_final: 0.8033 (mttm)
REVERT: B  736 ARG cc_start: 0.9027 (tmm-80) cc_final: 0.8783 (tpt-90)
REVERT: D   80 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7420 (m-80)
REVERT: D  108 MET cc_start: 0.8578 (tpp) cc_final: 0.8119 (mmm)
REVERT: C   73 ASP cc_start: 0.8162 (p0) cc_final: 0.7682 (p0)
REVERT: C   96 TYR cc_start: 0.7774 (m-80) cc_final: 0.7553 (m-80)
REVERT: C  123 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7802 (mm)
  outliers start: 15
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0835
  time to fit residues: 12.4407
Evaluate side-chains
  103 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue   80 TYR
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:   50.0000
   chunk 2 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 55 optimal weight:   30.0000
   chunk 65 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 71 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    1.7786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.103114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.081518 restraints weight = 30483.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.081508 restraints weight = 19775.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.082728 restraints weight = 14929.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.082814 restraints weight = 12321.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.082791 restraints weight = 10971.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8388  Z= 0.129
  Angle     :  0.529   8.497  11849  Z= 0.293
  Chirality :  0.037   0.180   1516
  Planarity :  0.003   0.041   1272
  Dihedral  : 16.025 163.313   2324
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.08 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 27.78 %
    Favored  : 68.83 %
  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:  2.30 (0.28), residues: 1008
  helix:  2.31 (0.21), residues: 645
  sheet: -0.80 (0.62), residues: 55
  loop :  0.37 (0.38), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  47 
 TYR   0.012   0.001   TYR C  96 
 PHE   0.016   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.13 ( 8388)
  covalent geometry    : angle       0.52851 /  0.29 (11849)
  hydrogen bonds       : bond        0.03871 /  2.65 (  570)
  hydrogen bonds       : angle       3.97127 /  3.02 ( 1576)

*********************** 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
  101 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.291 
Fit side-chains
REVERT: B  716 LYS cc_start: 0.8546 (mttt) cc_final: 0.8128 (mttm)
REVERT: B  736 ARG cc_start: 0.9081 (tmm-80) cc_final: 0.8743 (tpt-90)
REVERT: B  739 GLU cc_start: 0.8253 (pp20) cc_final: 0.7670 (pp20)
REVERT: D  108 MET cc_start: 0.8501 (tpp) cc_final: 0.8213 (mmm)
REVERT: C   73 ASP cc_start: 0.8134 (p0) cc_final: 0.7790 (p0)
REVERT: C   96 TYR cc_start: 0.7801 (m-80) cc_final: 0.7543 (m-80)
REVERT: C  123 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7641 (mm)
  outliers start: 11
  outliers final: 10
  residues processed: 99
  average time/residue: 0.0826
  time to fit residues: 11.5515
Evaluate side-chains
  97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0170
   chunk 91 optimal weight:   40.0000
   chunk 43 optimal weight:   50.0000
   chunk 41 optimal weight:    2.9990
   chunk 73 optimal weight:   50.0000
   chunk 56 optimal weight:    0.2980
   chunk 17 optimal weight:    5.9990
   chunk 72 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 55 optimal weight:   30.0000
   overall best weight:    2.6624

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 110 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.104752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.085500 restraints weight = 32273.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.085813 restraints weight = 22208.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.086421 restraints weight = 18235.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.086131 restraints weight = 14755.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.086306 restraints weight = 14781.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.3069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8388  Z= 0.166
  Angle     :  0.559   8.341  11849  Z= 0.309
  Chirality :  0.038   0.177   1516
  Planarity :  0.003   0.038   1272
  Dihedral  : 16.020 163.439   2324
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  2.78 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 27.78 %
    Favored  : 68.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.28), residues: 1008
  helix:  2.19 (0.21), residues: 655
  sheet: -0.71 (0.64), residues: 55
  loop :  0.31 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  47 
 TYR   0.014   0.002   TYR C 161 
 PHE   0.015   0.002   PHE C  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.003   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.17 ( 8388)
  covalent geometry    : angle       0.55852 /  0.31 (11849)
  hydrogen bonds       : bond        0.04190 /  2.87 (  570)
  hydrogen bonds       : angle       4.00967 /  3.04 ( 1576)

********************** 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
  104 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.282 
Fit side-chains
REVERT: B  716 LYS cc_start: 0.8514 (mttt) cc_final: 0.7974 (mttm)
REVERT: B  736 ARG cc_start: 0.9034 (tmm-80) cc_final: 0.8700 (tpt-90)
REVERT: B  739 GLU cc_start: 0.8185 (pp20) cc_final: 0.7630 (pp20)
REVERT: D  108 MET cc_start: 0.8540 (tpp) cc_final: 0.8157 (mmm)
REVERT: C   73 ASP cc_start: 0.8227 (p0) cc_final: 0.7769 (p0)
REVERT: C   96 TYR cc_start: 0.7820 (m-80) cc_final: 0.7564 (m-80)
REVERT: C  123 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7775 (mm)
  outliers start: 13
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0863
  time to fit residues: 12.3864
Evaluate side-chains
  100 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  734 THR
Chi-restraints excluded: chain D residue   26 GLU
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue   30 VAL
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  167 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:   30.0000
   chunk 39 optimal weight:    7.9990
   chunk 63 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   overall best weight:    1.1984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.105963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.086657 restraints weight = 32226.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.085572 restraints weight = 25835.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.086642 restraints weight = 19508.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.086640 restraints weight = 16790.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.086605 restraints weight = 14583.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8388  Z= 0.118
  Angle     :  0.533   9.423  11849  Z= 0.295
  Chirality :  0.036   0.179   1516
  Planarity :  0.003   0.040   1272
  Dihedral  : 16.047 163.716   2324
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  1.79 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 27.78 %
    Favored  : 68.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.31 (0.28), residues: 1008
  helix:  2.28 (0.21), residues: 654
  sheet: -0.68 (0.65), residues: 55
  loop :  0.39 (0.39), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  47 
 TYR   0.011   0.001   TYR C  96 
 PHE   0.014   0.002   PHE C  42 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.12 ( 8388)
  covalent geometry    : angle       0.53298 /  0.30 (11849)
  hydrogen bonds       : bond        0.03748 /  2.54 (  570)
  hydrogen bonds       : angle       3.91856 /  2.99 ( 1576)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1336.97 seconds
wall clock time: 23 minutes 45.35 seconds (1425.35 seconds total)