Starting phenix.real_space_refine
on Sun Apr  5 04:32:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rw2_54296/04_2026/9rw2_54296.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rw2_54296/04_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_54296/04_2026/9rw2_54296.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rw2_54296/04_2026/9rw2_54296.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rw2_54296/04_2026/9rw2_54296.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rw2_54296/04_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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.34, per 1000 atoms: 0.29
  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: 0.78
  Conformation dependent library (CDL) restraints added in 321.4 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: 1.09
  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: 1.39

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.21 -     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=" C   HIS C  31 "
       pdb=" O   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.236  1.211  0.026 1.26e-02 6.30e+03 4.15e+00
  bond pdb=" C   HIS C  31 "
       pdb=" N   ASP C  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.309  0.025 1.43e-02 4.89e+03 3.16e+00
  bond pdb=" CA  HIS C  31 "
       pdb=" C   HIS C  31 "
    ideal  model  delta    sigma   weight residual
    1.523  1.501  0.022 1.35e-02 5.49e+03 2.64e+00
  bond pdb=" N   GLN C 128 "
       pdb=" CA  GLN C 128 "
    ideal  model  delta    sigma   weight residual
    1.456  1.474 -0.018 1.32e-02 5.74e+03 1.94e+00
  bond pdb=" O3'   U F  11 "
       pdb=" P     U F  12 "
    ideal  model  delta    sigma   weight residual
    1.607  1.587  0.020 1.50e-02 4.44e+03 1.80e+00
  ... (remaining 8383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 10991
        1.18 -     2.36: 716
        2.36 -     3.54: 113
        3.54 -     4.72: 21
        4.72 -     5.90: 8
  Bond angle restraints: 11849
  Sorted by residual:
  angle pdb=" C4'   A F  10 "
        pdb=" C3'   A F  10 "
        pdb=" O3'   A F  10 "
      ideal   model   delta    sigma   weight residual
     113.00  107.82    5.18 1.50e+00 4.44e-01 1.19e+01
  angle pdb=" C5'   U F  11 "
        pdb=" C4'   U F  11 "
        pdb=" C3'   U F  11 "
      ideal   model   delta    sigma   weight residual
     116.00  111.03    4.97 1.50e+00 4.44e-01 1.10e+01
  angle pdb=" C4'   U F  11 "
        pdb=" C3'   U F  11 "
        pdb=" O3'   U F  11 "
      ideal   model   delta    sigma   weight residual
     113.00  108.27    4.73 1.50e+00 4.44e-01 9.96e+00
  angle pdb=" C5'   A F  10 "
        pdb=" C4'   A F  10 "
        pdb=" C3'   A F  10 "
      ideal   model   delta    sigma   weight residual
     116.00  111.58    4.42 1.50e+00 4.44e-01 8.67e+00
  angle pdb=" O3'   U F  11 "
        pdb=" P     U F  12 "
        pdb=" O5'   U F  12 "
      ideal   model   delta    sigma   weight residual
     104.00   99.71    4.29 1.50e+00 4.44e-01 8.19e+00
  ... (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 -    0.035: 1065
       0.035 -    0.069: 323
       0.069 -    0.104: 87
       0.104 -    0.138: 38
       0.138 -    0.173: 3
  Chirality restraints: 1516
  Sorted by residual:
  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
  chirality pdb=" C3'   C F  33 "
            pdb=" C4'   C F  33 "
            pdb=" O3'   C F  33 "
            pdb=" C2'   C F  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.17 2.00e-01 2.50e+01 7.25e-01
  chirality pdb=" C3'   C F   1 "
            pdb=" C4'   C F   1 "
            pdb=" O3'   C F   1 "
            pdb=" C2'   C F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.63    0.16 2.00e-01 2.50e+01 6.11e-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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.300
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
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= 0.174
  Angle     :  0.652   5.902  11849  Z= 0.370
  Chirality :  0.039   0.173   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
  covalent geometry    : bond        0.00304 ( 8388)
  covalent geometry    : angle       0.65196 (11849)
  hydrogen bonds       : bond        0.15592 (  570)
  hydrogen bonds       : angle       6.50985 ( 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  : 0.262 
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: 0.0972
  time to fit residues: 14.5829
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  : 0.289 
-------------------------------------------------------------------------------
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:    9.9990
   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:   10.0000
   overall best weight:    4.3024

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

Flipped N/Q/H residues before XYZ refinement:
C 110 GLN
C 128 GLN
C 132 GLN
C 139 GLN
C 151 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.101073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.079281 restraints weight = 30789.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.078873 restraints weight = 21220.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.079957 restraints weight = 16044.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.080348 restraints weight = 13065.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.080329 restraints weight = 11889.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8388  Z= 0.256
  Angle     :  0.623   8.990  11849  Z= 0.332
  Chirality :  0.040   0.201   1516
  Planarity :  0.004   0.033   1272
  Dihedral  : 16.272 160.760   2324
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.87 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 21.60 %
    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:  1.41 (0.27), residues: 1008
  helix:  1.71 (0.20), residues: 649
  sheet: -1.10 (0.66), residues: 52
  loop : -0.28 (0.38), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 724 
 TYR   0.015   0.002   TYR C  64 
 PHE   0.018   0.003   PHE C  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 8388)
  covalent geometry    : angle       0.62268 (11849)
  hydrogen bonds       : bond        0.04822 (  570)
  hydrogen bonds       : angle       4.63069 ( 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
  113 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  740 MET cc_start: 0.8379 (tmm) cc_final: 0.8154 (tmm)
REVERT: B  716 LYS cc_start: 0.8556 (mttt) cc_final: 0.8130 (mttm)
REVERT: C   73 ASP cc_start: 0.8142 (p0) cc_final: 0.7672 (p0)
REVERT: C   96 TYR cc_start: 0.8230 (m-80) cc_final: 0.8013 (m-80)
REVERT: C  102 ASP cc_start: 0.8170 (m-30) cc_final: 0.7926 (p0)
REVERT: C  123 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7870 (mm)
REVERT: C  139 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8120 (tp-100)
  outliers start: 20
  outliers final: 12
  residues processed: 109
  average time/residue: 0.0855
  time to fit residues: 13.0209
Evaluate side-chains
  97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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   34 SER
Chi-restraints excluded: chain D residue  117 VAL
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain D residue  165 VAL
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  139 GLN
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:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:   20.0000
   chunk 20 optimal weight:    0.7980
   chunk 29 optimal weight:   30.0000
   chunk 4 optimal weight:    5.9990
   chunk 47 optimal weight:   30.0000
   chunk 59 optimal weight:    0.6980
   chunk 106 optimal weight:   10.0000
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.105448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.082764 restraints weight = 32042.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.084749 restraints weight = 20730.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.084929 restraints weight = 14580.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.084832 restraints weight = 14093.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.085008 restraints weight = 14217.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8388  Z= 0.135
  Angle     :  0.506   9.440  11849  Z= 0.268
  Chirality :  0.036   0.170   1516
  Planarity :  0.003   0.030   1272
  Dihedral  : 16.202 162.312   2324
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.38 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 22.53 %
    Favored  : 72.53 %
  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:  2.15 (0.28), residues: 1008
  helix:  2.29 (0.21), residues: 647
  sheet: -1.06 (0.60), residues: 55
  loop :  0.09 (0.38), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 126 
 TYR   0.010   0.001   TYR C  64 
 PHE   0.016   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
  covalent geometry    : bond        0.00284 ( 8388)
  covalent geometry    : angle       0.50647 (11849)
  hydrogen bonds       : bond        0.03725 (  570)
  hydrogen bonds       : angle       4.07870 ( 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
  110 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: B  716 LYS cc_start: 0.8508 (mttt) cc_final: 0.8041 (mttm)
REVERT: B  736 ARG cc_start: 0.9020 (tmm-80) cc_final: 0.8782 (tpt-90)
REVERT: C   46 MET cc_start: 0.8259 (mtp) cc_final: 0.7993 (mtp)
REVERT: C   73 ASP cc_start: 0.8006 (p0) cc_final: 0.7613 (p0)
REVERT: C  102 ASP cc_start: 0.8205 (m-30) cc_final: 0.7823 (p0)
REVERT: C  116 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7593 (mm-30)
REVERT: C  123 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7673 (mm)
REVERT: C  163 MET cc_start: 0.5513 (mtm) cc_final: 0.5009 (mmm)
  outliers start: 16
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0866
  time to fit residues: 12.6971
Evaluate side-chains
  97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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  117 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue  110 GLN
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 67 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 104 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 58 optimal weight:    0.8980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
D 128 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.106215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.085603 restraints weight = 32555.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.084994 restraints weight = 25583.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.085913 restraints weight = 19545.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.086376 restraints weight = 15863.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.086359 restraints weight = 13709.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8388  Z= 0.112
  Angle     :  0.486   6.651  11849  Z= 0.255
  Chirality :  0.035   0.162   1516
  Planarity :  0.003   0.033   1272
  Dihedral  : 16.077 161.212   2324
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.08 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.38 %
    Favored  : 71.91 %
  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:  2.40 (0.28), residues: 1008
  helix:  2.48 (0.21), residues: 650
  sheet: -0.92 (0.60), residues: 55
  loop :  0.15 (0.38), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  47 
 TYR   0.009   0.001   TYR C  64 
 PHE   0.013   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.000   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8388)
  covalent geometry    : angle       0.48597 (11849)
  hydrogen bonds       : bond        0.03313 (  570)
  hydrogen bonds       : angle       3.80360 ( 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: 12
    poor density    : 100
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
REVERT: A  717 LYS cc_start: 0.8581 (tttp) cc_final: 0.8337 (tttt)
REVERT: B  716 LYS cc_start: 0.8549 (mttt) cc_final: 0.8180 (mttm)
REVERT: B  736 ARG cc_start: 0.8978 (tmm-80) cc_final: 0.8749 (tpt-90)
REVERT: D  106 ASN cc_start: 0.8555 (m-40) cc_final: 0.8188 (m-40)
REVERT: C   73 ASP cc_start: 0.7907 (p0) cc_final: 0.7661 (p0)
REVERT: C   98 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8188 (pp30)
REVERT: C  116 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7544 (mm-30)
REVERT: C  123 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7827 (mm)
REVERT: C  126 ARG cc_start: 0.7733 (tmt170) cc_final: 0.6819 (tmm-80)
REVERT: C  153 ASP cc_start: 0.7801 (p0) cc_final: 0.7441 (t0)
REVERT: C  163 MET cc_start: 0.5326 (mtm) cc_final: 0.4905 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0894
  time to fit residues: 13.3807
Evaluate side-chains
  102 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
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  117 VAL
Chi-restraints excluded: chain C residue   12 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  110 GLN
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  123 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 90 optimal weight:   50.0000
   chunk 13 optimal weight:    0.0370
   chunk 46 optimal weight:   20.0000
   chunk 93 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 84 optimal weight:    8.9990
   chunk 42 optimal weight:    0.0270
   chunk 89 optimal weight:   40.0000
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.9720

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.106745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.087699 restraints weight = 31765.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.086175 restraints weight = 25117.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.087332 restraints weight = 19790.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.087421 restraints weight = 16100.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.087386 restraints weight = 13540.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8388  Z= 0.103
  Angle     :  0.485   7.282  11849  Z= 0.253
  Chirality :  0.035   0.198   1516
  Planarity :  0.003   0.035   1272
  Dihedral  : 16.009 161.118   2324
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.59 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 24.38 %
    Favored  : 71.91 %
  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:  2.57 (0.28), residues: 1008
  helix:  2.60 (0.21), residues: 650
  sheet: -0.74 (0.63), residues: 55
  loop :  0.23 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  47 
 TYR   0.011   0.001   TYR C 161 
 PHE   0.011   0.001   PHE C 144 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.001   0.000   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 8388)
  covalent geometry    : angle       0.48455 (11849)
  hydrogen bonds       : bond        0.03029 (  570)
  hydrogen bonds       : angle       3.64982 ( 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: 12
    poor density    : 97
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  716 LYS cc_start: 0.8542 (mttt) cc_final: 0.8142 (mttm)
REVERT: B  736 ARG cc_start: 0.8949 (tmm-80) cc_final: 0.8706 (tpt-90)
REVERT: C   96 TYR cc_start: 0.7689 (m-80) cc_final: 0.7415 (m-80)
REVERT: C  116 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7353 (mm-30)
REVERT: C  123 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7832 (mm)
REVERT: C  126 ARG cc_start: 0.7690 (tmt170) cc_final: 0.6777 (tmm-80)
REVERT: C  149 MET cc_start: 0.8054 (mtp) cc_final: 0.7106 (ppp)
REVERT: C  163 MET cc_start: 0.5250 (mtm) cc_final: 0.4510 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0874
  time to fit residues: 12.9669
Evaluate side-chains
  102 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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 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  110 GLN
Chi-restraints excluded: chain C residue  116 GLU
Chi-restraints excluded: chain C residue  123 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 81 optimal weight:   30.0000
   chunk 44 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 79 optimal weight:   50.0000
   chunk 63 optimal weight:    0.0010
   chunk 40 optimal weight:    0.9990
   chunk 94 optimal weight:   30.0000
   chunk 37 optimal weight:   30.0000
   chunk 25 optimal weight:    0.0670
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.5524

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.107262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.088281 restraints weight = 30955.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.086816 restraints weight = 21926.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.087503 restraints weight = 18618.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.087545 restraints weight = 16923.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.087563 restraints weight = 15783.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8388  Z= 0.092
  Angle     :  0.466   7.557  11849  Z= 0.245
  Chirality :  0.035   0.191   1516
  Planarity :  0.003   0.035   1272
  Dihedral  : 15.905 160.709   2324
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.59 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 23.77 %
    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:  2.75 (0.28), residues: 1008
  helix:  2.71 (0.20), residues: 650
  sheet: -0.36 (0.67), residues: 55
  loop :  0.30 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  47 
 TYR   0.011   0.001   TYR C  74 
 PHE   0.012   0.001   PHE C 144 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.001   0.000   HIS D 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00184 ( 8388)
  covalent geometry    : angle       0.46571 (11849)
  hydrogen bonds       : bond        0.02733 (  570)
  hydrogen bonds       : angle       3.48198 ( 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
  118 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  713 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7443 (tm-30)
REVERT: A  737 LEU cc_start: 0.8622 (tt) cc_final: 0.8349 (tp)
REVERT: B  716 LYS cc_start: 0.8540 (mttt) cc_final: 0.8075 (mttm)
REVERT: B  736 ARG cc_start: 0.8967 (tmm-80) cc_final: 0.8648 (tpt-90)
REVERT: C   98 GLN cc_start: 0.8688 (pp30) cc_final: 0.8474 (pp30)
REVERT: C  116 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7322 (mm-30)
REVERT: C  126 ARG cc_start: 0.7548 (tmt170) cc_final: 0.6688 (tmm-80)
REVERT: C  149 MET cc_start: 0.8017 (mtp) cc_final: 0.7018 (ppp)
REVERT: C  153 ASP cc_start: 0.7908 (p0) cc_final: 0.7496 (t0)
REVERT: C  163 MET cc_start: 0.5202 (mtm) cc_final: 0.4420 (mmm)
  outliers start: 13
  outliers final: 8
  residues processed: 115
  average time/residue: 0.0859
  time to fit residues: 13.6325
Evaluate side-chains
  102 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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 B residue  735 GLN
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 82 optimal weight:    9.9990
   chunk 33 optimal weight:   20.0000
   chunk 104 optimal weight:   10.0000
   chunk 88 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 721 GLN
D 106 ASN
D 135 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.103489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.083855 restraints weight = 31112.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.081847 restraints weight = 23638.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.082578 restraints weight = 21731.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.082785 restraints weight = 17841.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.082643 restraints weight = 16581.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8388  Z= 0.198
  Angle     :  0.575  12.290  11849  Z= 0.301
  Chirality :  0.038   0.183   1516
  Planarity :  0.003   0.038   1272
  Dihedral  : 16.159 162.263   2324
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.58 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 25.93 %
    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:  2.63 (0.28), residues: 1008
  helix:  2.56 (0.21), residues: 649
  sheet: -0.40 (0.70), residues: 55
  loop :  0.42 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 724 
 TYR   0.015   0.002   TYR C 161 
 PHE   0.016   0.003   PHE C  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 8388)
  covalent geometry    : angle       0.57510 (11849)
  hydrogen bonds       : bond        0.03910 (  570)
  hydrogen bonds       : angle       3.86010 ( 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
  106 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  717 LYS cc_start: 0.8663 (tttp) cc_final: 0.8409 (tttt)
REVERT: B  716 LYS cc_start: 0.8594 (mttt) cc_final: 0.8101 (mttm)
REVERT: B  736 ARG cc_start: 0.9007 (tmm-80) cc_final: 0.8802 (tpt-90)
REVERT: D  108 MET cc_start: 0.8395 (tpp) cc_final: 0.8081 (mmm)
REVERT: C  116 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7537 (mm-30)
REVERT: C  122 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8319 (mm)
REVERT: C  149 MET cc_start: 0.7967 (mtp) cc_final: 0.7147 (ppp)
REVERT: C  163 MET cc_start: 0.5486 (mtm) cc_final: 0.4673 (mmm)
  outliers start: 13
  outliers final: 7
  residues processed: 102
  average time/residue: 0.0895
  time to fit residues: 12.4960
Evaluate side-chains
  96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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 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
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:    0.7980
   chunk 55 optimal weight:   30.0000
   chunk 88 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0010
   chunk 99 optimal weight:    0.0040
   chunk 53 optimal weight:   20.0000
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
B 721 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.105145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.085116 restraints weight = 30689.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.083399 restraints weight = 24841.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.084073 restraints weight = 19383.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.084304 restraints weight = 17655.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.084124 restraints weight = 15944.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3819

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= 0.113
  Angle     :  0.524  10.361  11849  Z= 0.273
  Chirality :  0.035   0.181   1516
  Planarity :  0.003   0.035   1272
  Dihedral  : 16.086 161.930   2324
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.98 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 27.78 %
    Favored  : 68.52 %
  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:  2.72 (0.28), residues: 1008
  helix:  2.64 (0.21), residues: 648
  sheet: -0.36 (0.71), residues: 55
  loop :  0.44 (0.39), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 724 
 TYR   0.017   0.001   TYR C  96 
 PHE   0.011   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.000   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 8388)
  covalent geometry    : angle       0.52395 (11849)
  hydrogen bonds       : bond        0.03209 (  570)
  hydrogen bonds       : angle       3.66354 ( 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
  104 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  717 LYS cc_start: 0.8520 (tttp) cc_final: 0.8301 (tttt)
REVERT: B  716 LYS cc_start: 0.8558 (mttt) cc_final: 0.8100 (mttm)
REVERT: B  728 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7507 (mt0)
REVERT: B  736 ARG cc_start: 0.9045 (tmm-80) cc_final: 0.8629 (tpt-90)
REVERT: B  739 GLU cc_start: 0.8212 (pp20) cc_final: 0.7624 (pp20)
REVERT: D  108 MET cc_start: 0.8204 (tpp) cc_final: 0.7944 (mmm)
REVERT: C  116 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7322 (mm-30)
REVERT: C  149 MET cc_start: 0.7933 (mtp) cc_final: 0.7145 (ppp)
REVERT: C  163 MET cc_start: 0.5320 (mtm) cc_final: 0.4547 (mmm)
  outliers start: 12
  outliers final: 5
  residues processed: 100
  average time/residue: 0.0872
  time to fit residues: 12.0565
Evaluate side-chains
  96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue   12 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  116 GLU
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:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 86 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:   30.0000
   chunk 65 optimal weight:    4.9990
   chunk 84 optimal weight:   20.0000
   chunk 71 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 94 optimal weight:    9.9990
   overall best weight:    2.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.103871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.083416 restraints weight = 30735.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.082242 restraints weight = 23336.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.082728 restraints weight = 19339.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.083075 restraints weight = 17115.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.082998 restraints weight = 15501.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8388  Z= 0.162
  Angle     :  0.562   7.530  11849  Z= 0.297
  Chirality :  0.037   0.172   1516
  Planarity :  0.003   0.037   1272
  Dihedral  : 16.130 162.512   2324
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.58 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 28.09 %
    Favored  : 69.44 %
  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:  2.70 (0.28), residues: 1008
  helix:  2.60 (0.21), residues: 648
  sheet: -0.35 (0.72), residues: 55
  loop :  0.48 (0.39), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 724 
 TYR   0.011   0.001   TYR C  64 
 PHE   0.014   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
  covalent geometry    : bond        0.00347 ( 8388)
  covalent geometry    : angle       0.56171 (11849)
  hydrogen bonds       : bond        0.03585 (  570)
  hydrogen bonds       : angle       3.76621 ( 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
  100 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  717 LYS cc_start: 0.8628 (tttp) cc_final: 0.8356 (tttt)
REVERT: B  716 LYS cc_start: 0.8592 (mttt) cc_final: 0.8124 (mttm)
REVERT: B  728 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7659 (mt0)
REVERT: C  116 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7507 (mm-30)
REVERT: C  149 MET cc_start: 0.7803 (mtp) cc_final: 0.7200 (ppp)
REVERT: C  163 MET cc_start: 0.5290 (mtm) cc_final: 0.4511 (mmm)
  outliers start: 8
  outliers final: 5
  residues processed: 99
  average time/residue: 0.0846
  time to fit residues: 11.5165
Evaluate side-chains
  95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue   12 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  116 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 43 optimal weight:   40.0000
   chunk 41 optimal weight:   30.0000
   chunk 73 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 72 optimal weight:   20.0000
   chunk 32 optimal weight:   10.0000
   chunk 55 optimal weight:   30.0000
   overall best weight:    2.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.102377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.082384 restraints weight = 30873.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.081202 restraints weight = 22983.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.081728 restraints weight = 19279.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.081991 restraints weight = 18041.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.081812 restraints weight = 15414.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8388  Z= 0.189
  Angle     :  0.588   7.500  11849  Z= 0.312
  Chirality :  0.038   0.166   1516
  Planarity :  0.003   0.034   1272
  Dihedral  : 16.294 163.479   2324
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.08 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 27.47 %
    Favored  : 70.37 %
  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:  2.59 (0.28), residues: 1008
  helix:  2.48 (0.20), residues: 648
  sheet: -0.37 (0.73), residues: 54
  loop :  0.51 (0.40), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 724 
 TYR   0.020   0.001   TYR C  96 
 PHE   0.016   0.002   PHE C 104 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.004   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8388)
  covalent geometry    : angle       0.58825 (11849)
  hydrogen bonds       : bond        0.03972 (  570)
  hydrogen bonds       : angle       3.91067 ( 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
  96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  716 LYS cc_start: 0.8585 (mttt) cc_final: 0.8131 (mttm)
REVERT: C  116 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7666 (mm-30)
REVERT: C  163 MET cc_start: 0.5216 (mtm) cc_final: 0.4594 (mmm)
  outliers start: 7
  outliers final: 6
  residues processed: 95
  average time/residue: 0.0907
  time to fit residues: 11.8565
Evaluate side-chains
  93 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 C residue   12 MET
Chi-restraints excluded: chain C residue   29 THR
Chi-restraints excluded: chain C residue  116 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 63 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 32 optimal weight:   30.0000
   chunk 31 optimal weight:   40.0000
   chunk 67 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 81 optimal weight:   50.0000
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.102531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.080145 restraints weight = 29714.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.080591 restraints weight = 21293.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.080956 restraints weight = 15989.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.081386 restraints weight = 14335.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.081590 restraints weight = 11871.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8388  Z= 0.119
  Angle     :  0.533   7.691  11849  Z= 0.282
  Chirality :  0.036   0.168   1516
  Planarity :  0.003   0.033   1272
  Dihedral  : 16.165 162.758   2324
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.38 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 27.47 %
    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:  2.87 (0.28), residues: 1008
  helix:  2.71 (0.21), residues: 647
  sheet: -0.14 (0.78), residues: 48
  loop :  0.57 (0.40), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  47 
 TYR   0.014   0.001   TYR C  96 
 PHE   0.011   0.001   PHE D  17 
 TRP   0.000   0.000   TRP D 522 
 HIS   0.002   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8388)
  covalent geometry    : angle       0.53275 (11849)
  hydrogen bonds       : bond        0.03279 (  570)
  hydrogen bonds       : angle       3.65754 ( 1576)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1389.53 seconds
wall clock time: 24 minutes 37.42 seconds (1477.42 seconds total)