Starting phenix.real_space_refine
on Fri Sep 11 20:59:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/26ci_80538/09_2026/26ci_80538.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/26ci_80538/09_2026/26ci_80538.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/26ci_80538/09_2026/26ci_80538.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/26ci_80538/09_2026/26ci_80538.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/26ci_80538/09_2026/26ci_80538.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/26ci_80538/09_2026/26ci_80538.map"
  }
  resolution = 2.63
  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=  -0.001 sd=   0.076
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: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    7086      2.51       5
     N    2031      2.21       5
     O    2187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11319
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3773
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 462}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3773
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 462}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 3773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3773
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 462}
          Chain breaks: 1
  Time building chain proxies: 2.64, per 1000 atoms: 0.23
  Number of scatterers: 11319
  At special positions: 0
  Unit cell: (105.564, 104.638, 186.126, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O    2187      8.00
     N    2031      7.00
     C    7086      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: 0.82
  Conformation dependent library (CDL) restraints added in 404.3 milliseconds
  

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 30 sheets defined
      9.6% alpha, 41.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 49
      No H-bonds generated for 'chain 'A' and resid 47 through 49'
    Processing helix  chain 'A' and resid 763 through 767
    Processing helix  chain 'A' and resid 818 through 826
      removed outlier: 3.701A  pdb=" N   TYR A 822 " --> pdb=" O   ASP A 818 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   GLN A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU A 825 " --> pdb=" O   GLU A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 836
    Processing helix  chain 'A' and resid 836 through 856
      removed outlier: 4.008A  pdb=" N   PHE A 840 " --> pdb=" O   GLY A 836 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY A 851 " --> pdb=" O   GLN A 847 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 49
      No H-bonds generated for 'chain 'C' and resid 47 through 49'
    Processing helix  chain 'C' and resid 763 through 767
      removed outlier: 3.501A  pdb=" N   ALA C 767 " --> pdb=" O   GLU C 764 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 818 through 826
      removed outlier: 3.670A  pdb=" N   TYR C 822 " --> pdb=" O   ASP C 818 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   GLN C 824 " --> pdb=" O   SER C 820 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   LEU C 825 " --> pdb=" O   GLU C 821 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 827 through 836
    Processing helix  chain 'C' and resid 836 through 856
      removed outlier: 4.128A  pdb=" N   PHE C 840 " --> pdb=" O   GLY C 836 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 47 through 49
      No H-bonds generated for 'chain 'G' and resid 47 through 49'
    Processing helix  chain 'G' and resid 763 through 767
    Processing helix  chain 'G' and resid 818 through 823
      removed outlier: 3.716A  pdb=" N   TYR G 822 " --> pdb=" O   ASP G 818 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 827 through 836
    Processing helix  chain 'G' and resid 836 through 856
      removed outlier: 4.033A  pdb=" N   PHE G 840 " --> pdb=" O   GLY G 836 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY G 851 " --> pdb=" O   GLN G 847 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 39
      removed outlier: 6.527A  pdb=" N   ALA A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53
    Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 99
      removed outlier: 4.441A  pdb=" N   VAL A  90 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   GLU A 208 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   VAL A  98 " --> pdb=" O   ARG A 206 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   ARG A 206 " --> pdb=" O   VAL A  98 " (cutoff:3.500A)
      removed outlier: 5.467A  pdb=" N   VAL A 207 " --> pdb=" O   SER A 123 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   SER A 123 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 209 " --> pdb=" O   ARG A 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 110
      removed outlier: 6.594A  pdb=" N   ILE A 147 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   GLU A 156 " --> pdb=" O   ILE A 147 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 137
    Processing sheet with id=AA6, first strand: chain 'A' and resid 628 through 636
      removed outlier: 6.519A  pdb=" N   THR A 642 " --> pdb=" O   GLY A 683 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 669 through 674
      removed outlier: 4.303A  pdb=" N   ALA A 659 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   ARG A 673 " --> pdb=" O   TYR A 657 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR A 657 " --> pdb=" O   ARG A 673 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 669 through 674
      removed outlier: 4.303A  pdb=" N   ALA A 659 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   ARG A 673 " --> pdb=" O   TYR A 657 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   TYR A 657 " --> pdb=" O   ARG A 673 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 725 through 731
      removed outlier: 3.628A  pdb=" N   TYR A 725 " --> pdb=" O   GLY A 740 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 768 through 774
      removed outlier: 6.662A  pdb=" N   ILE A 754 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   LEU A 772 " --> pdb=" O   THR A 752 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   THR A 752 " --> pdb=" O   LEU A 772 " (cutoff:3.500A)
      removed outlier: 4.909A  pdb=" N   ALA A 774 " --> pdb=" O   ALA A 750 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   ALA A 750 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 39
      removed outlier: 6.520A  pdb=" N   ALA C 224 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 51 through 53
    Processing sheet with id=AB4, first strand: chain 'C' and resid 88 through 99
      removed outlier: 4.445A  pdb=" N   VAL C  90 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   GLU C 208 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL C  98 " --> pdb=" O   ARG C 206 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ARG C 206 " --> pdb=" O   VAL C  98 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   VAL C 207 " --> pdb=" O   SER C 123 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   SER C 123 " --> pdb=" O   VAL C 207 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ALA C 209 " --> pdb=" O   ARG C 121 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 106 through 110
      removed outlier: 6.564A  pdb=" N   ILE C 147 " --> pdb=" O   GLU C 156 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   GLU C 156 " --> pdb=" O   ILE C 147 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 137
    Processing sheet with id=AB7, first strand: chain 'C' and resid 625 through 636
      removed outlier: 3.907A  pdb=" N   GLN C 625 " --> pdb=" O   ASP C 649 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   VAL C 627 " --> pdb=" O   SER C 647 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   SER C 647 " --> pdb=" O   VAL C 627 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ILE C 629 " --> pdb=" O   SER C 645 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   SER C 645 " --> pdb=" O   ILE C 629 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ALA C 631 " --> pdb=" O   SER C 643 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   SER C 643 " --> pdb=" O   ALA C 631 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   THR C 633 " --> pdb=" O   VAL C 641 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   VAL C 641 " --> pdb=" O   THR C 633 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   VAL C 635 " --> pdb=" O   LEU C 639 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LEU C 639 " --> pdb=" O   VAL C 635 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   THR C 642 " --> pdb=" O   GLY C 683 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 669 through 674
      removed outlier: 4.279A  pdb=" N   ALA C 659 " --> pdb=" O   VAL C 671 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ARG C 673 " --> pdb=" O   TYR C 657 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   TYR C 657 " --> pdb=" O   ARG C 673 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 669 through 674
      removed outlier: 4.279A  pdb=" N   ALA C 659 " --> pdb=" O   VAL C 671 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   ARG C 673 " --> pdb=" O   TYR C 657 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   TYR C 657 " --> pdb=" O   ARG C 673 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 725 through 731
      removed outlier: 3.654A  pdb=" N   TYR C 725 " --> pdb=" O   GLY C 740 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 768 through 774
      removed outlier: 6.655A  pdb=" N   ILE C 754 " --> pdb=" O   LEU C 770 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   LEU C 772 " --> pdb=" O   THR C 752 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   THR C 752 " --> pdb=" O   LEU C 772 " (cutoff:3.500A)
      removed outlier: 4.872A  pdb=" N   ALA C 774 " --> pdb=" O   ALA C 750 " (cutoff:3.500A)
      removed outlier: 7.839A  pdb=" N   ALA C 750 " --> pdb=" O   ALA C 774 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'G' and resid 30 through 39
      removed outlier: 6.537A  pdb=" N   ALA G 224 " --> pdb=" O   LEU G  37 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'G' and resid 56 through 57
    Processing sheet with id=AC5, first strand: chain 'G' and resid 88 through 99
      removed outlier: 4.570A  pdb=" N   VAL G  90 " --> pdb=" O   ILE G 214 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   GLU G 208 " --> pdb=" O   VAL G  96 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   VAL G  98 " --> pdb=" O   ARG G 206 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   ARG G 206 " --> pdb=" O   VAL G  98 " (cutoff:3.500A)
      removed outlier: 5.483A  pdb=" N   VAL G 207 " --> pdb=" O   SER G 123 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   SER G 123 " --> pdb=" O   VAL G 207 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ALA G 209 " --> pdb=" O   ARG G 121 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'G' and resid 106 through 110
      removed outlier: 6.585A  pdb=" N   ILE G 147 " --> pdb=" O   GLU G 156 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   GLU G 156 " --> pdb=" O   ILE G 147 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'G' and resid 136 through 137
    Processing sheet with id=AC8, first strand: chain 'G' and resid 628 through 636
      removed outlier: 6.489A  pdb=" N   THR G 642 " --> pdb=" O   GLY G 683 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'G' and resid 669 through 674
      removed outlier: 4.296A  pdb=" N   ALA G 659 " --> pdb=" O   VAL G 671 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   ARG G 673 " --> pdb=" O   TYR G 657 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   TYR G 657 " --> pdb=" O   ARG G 673 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'G' and resid 669 through 674
      removed outlier: 4.296A  pdb=" N   ALA G 659 " --> pdb=" O   VAL G 671 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   ARG G 673 " --> pdb=" O   TYR G 657 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   TYR G 657 " --> pdb=" O   ARG G 673 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'G' and resid 725 through 731
      removed outlier: 3.734A  pdb=" N   TYR G 725 " --> pdb=" O   GLY G 740 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'G' and resid 768 through 774
      removed outlier: 6.644A  pdb=" N   ILE G 754 " --> pdb=" O   LEU G 770 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   LEU G 772 " --> pdb=" O   THR G 752 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   THR G 752 " --> pdb=" O   LEU G 772 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   ALA G 774 " --> pdb=" O   ALA G 750 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   ALA G 750 " --> pdb=" O   ALA G 774 " (cutoff:3.500A)

    448 hydrogen bonds defined for protein.
    1170 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3900
        1.34 -     1.46: 2023
        1.46 -     1.57: 5615
        1.57 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 11565
  Sorted by residual:
  bond pdb=" CA  GLU G 700 "
       pdb=" CB  GLU G 700 "
    ideal  model  delta    sigma   weight residual
    1.530  1.551 -0.021 1.69e-02 3.50e+03 1.48e+00
  bond pdb=" CB  ASP G  55 "
       pdb=" CG  ASP G  55 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.40e+00
  bond pdb=" CB  LYS A   9 "
       pdb=" CG  LYS A   9 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.30e+00
  bond pdb=" CA  GLU A 700 "
       pdb=" CB  GLU A 700 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.28e+00
  bond pdb=" CA  LYS A   9 "
       pdb=" CB  LYS A   9 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.69e-02 3.50e+03 1.22e+00
  ... (remaining 11560 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 15427
        1.75 -     3.50: 272
        3.50 -     5.25: 38
        5.25 -     7.00: 9
        7.00 -     8.74: 4
  Bond angle restraints: 15750
  Sorted by residual:
  angle pdb=" N   ASP A  23 "
        pdb=" CA  ASP A  23 "
        pdb=" C   ASP A  23 "
      ideal   model   delta    sigma   weight residual
     114.56  108.98    5.58 1.27e+00 6.20e-01 1.93e+01
  angle pdb=" CA  LYS A   9 "
        pdb=" CB  LYS A   9 "
        pdb=" CG  LYS A   9 "
      ideal   model   delta    sigma   weight residual
     114.10  122.84   -8.74 2.00e+00 2.50e-01 1.91e+01
  angle pdb=" CA  GLU G 700 "
        pdb=" CB  GLU G 700 "
        pdb=" CG  GLU G 700 "
      ideal   model   delta    sigma   weight residual
     114.10  121.87   -7.77 2.00e+00 2.50e-01 1.51e+01
  angle pdb=" CA  GLU A 700 "
        pdb=" CB  GLU A 700 "
        pdb=" CG  GLU A 700 "
      ideal   model   delta    sigma   weight residual
     114.10  121.19   -7.09 2.00e+00 2.50e-01 1.26e+01
  angle pdb=" C   THR A   6 "
        pdb=" N   GLY A   7 "
        pdb=" CA  GLY A   7 "
      ideal   model   delta    sigma   weight residual
     120.07  126.11   -6.04 1.95e+00 2.63e-01 9.60e+00
  ... (remaining 15745 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 6002
       17.98 -    35.95: 637
       35.95 -    53.93: 217
       53.93 -    71.90: 40
       71.90 -    89.88: 13
  Dihedral angle restraints: 6909
    sinusoidal: 2709
      harmonic: 4200
  Sorted by residual:
  dihedral pdb=" CA  ASP A 636 "
           pdb=" C   ASP A 636 "
           pdb=" N   GLN A 637 "
           pdb=" CA  GLN A 637 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.93  -25.07     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  ASP C 636 "
           pdb=" C   ASP C 636 "
           pdb=" N   GLN C 637 "
           pdb=" CA  GLN C 637 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.98  -25.02     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  ASP G 636 "
           pdb=" C   ASP G 636 "
           pdb=" N   GLN G 637 "
           pdb=" CA  GLN G 637 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.02  -24.98     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 6906 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1354
       0.047 -    0.094: 237
       0.094 -    0.141: 128
       0.141 -    0.188: 3
       0.188 -    0.234: 6
  Chirality restraints: 1728
  Sorted by residual:
  chirality pdb=" CB  ILE A   5 "
            pdb=" CA  ILE A   5 "
            pdb=" CG1 ILE A   5 "
            pdb=" CG2 ILE A   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" CB  ILE C   5 "
            pdb=" CA  ILE C   5 "
            pdb=" CG1 ILE C   5 "
            pdb=" CG2 ILE C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  GLU G 700 "
            pdb=" N   GLU G 700 "
            pdb=" C   GLU G 700 "
            pdb=" CB  GLU G 700 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1725 not shown)

  Planarity restraints: 2097
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET C  21 "   -0.042 5.00e-02 4.00e+02   6.49e-02 6.74e+00
        pdb=" N   PRO C  22 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO C  22 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C  22 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A   9 "    0.011 2.00e-02 2.50e+03   2.23e-02 4.96e+00
        pdb=" C   LYS A   9 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   LYS A   9 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLY A  10 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU G 700 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.44e+00
        pdb=" CD  GLU G 700 "   -0.032 2.00e-02 2.50e+03
        pdb=" OE1 GLU G 700 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU G 700 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2094 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 128
        2.65 -     3.21: 9557
        3.21 -     3.77: 16856
        3.77 -     4.34: 23992
        4.34 -     4.90: 40001
  Nonbonded interactions: 90534
  Sorted by model distance:
  nonbonded pdb=" OG  SER G 763 "
            pdb=" OE1 GLU G 765 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" O   SER A 615 "
            pdb=" OG  SER A 615 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   TYR G 685 "
            pdb=" OH  TYR G 689 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   TYR A 685 "
            pdb=" OH  TYR A 689 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   TYR C 685 "
            pdb=" OH  TYR C 689 "
     model   vdw
     2.261 3.040
  ... (remaining 90529 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'G'
}

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 individual isotropic
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:             4.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.040
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:5.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
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   0.034  11565  Z= 0.123
  Angle     :  0.583   8.744  15750  Z= 0.311
  Chirality :  0.047   0.234   1728
  Planarity :  0.004   0.065   2097
  Dihedral  : 17.021  89.879   4221
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.87 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 26.73 %
    Favored  : 69.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.08 (0.22), residues: 1464
  helix:  0.05 (0.49), residues: 108
  sheet:  1.01 (0.20), residues: 576
  loop : -0.92 (0.23), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 121 
 TYR   0.008   0.001   TYR A 751 
 PHE   0.008   0.001   PHE A 235 
 TRP   0.010   0.001   TRP G 739 
 HIS   0.001   0.000   HIS C 780 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.12 (11565)
  covalent geometry    : angle       0.58320 /  0.31 (15750)
  hydrogen bonds       : bond        0.12679 /  7.92 (  415)
  hydrogen bonds       : angle       6.61862 /  4.60 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 113
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
  outliers start: 43
  outliers final: 29
  residues processed: 155
  average time/residue: 0.4045
  time to fit residues: 70.2816
Evaluate side-chains
  138 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   55 ASP
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  233 SER
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  629 ILE
Chi-restraints excluded: chain C residue  711 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  801 SER
Chi-restraints excluded: chain C residue  853 LEU
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue   90 VAL
Chi-restraints excluded: chain G residue  123 SER
Chi-restraints excluded: chain G residue  233 SER
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  633 THR
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  711 THR
Chi-restraints excluded: chain G residue  791 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   overall best weight:    1.2182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
A 625 GLN
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.188225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.117555 restraints weight = 13267.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.59
r_work: 0.3254 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3141 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.0635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11565  Z= 0.171
  Angle     :  0.596   6.292  15750  Z= 0.315
  Chirality :  0.047   0.204   1728
  Planarity :  0.004   0.049   2097
  Dihedral  :  6.290  50.968   1662
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.94 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 22.67 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.08 (0.21), residues: 1464
  helix:  0.49 (0.51), residues: 108
  sheet:  0.99 (0.20), residues: 558
  loop : -0.92 (0.22), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 121 
 TYR   0.011   0.002   TYR G 685 
 PHE   0.013   0.002   PHE A 773 
 TRP   0.014   0.002   TRP C 807 
 HIS   0.001   0.001   HIS A 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.17 (11565)
  covalent geometry    : angle       0.59605 /  0.32 (15750)
  hydrogen bonds       : bond        0.03579 /  2.39 (  415)
  hydrogen bonds       : angle       5.69830 /  3.96 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 123
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A   99 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6902 (tm-30)
REVERT: A  838 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6238 (tm-30)
REVERT: C  190 ARG cc_start: 0.7417 (mtm110) cc_final: 0.6782 (mtm180)
REVERT: C  838 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6312 (tm-30)
REVERT: G    9 LYS cc_start: 0.4374 (OUTLIER) cc_final: 0.3718 (pptt)
REVERT: G   91 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6693 (mt-10)
REVERT: G  119 ARG cc_start: 0.6530 (ttm110) cc_final: 0.6315 (mtm110)
REVERT: G  838 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.5867 (tm-30)
  outliers start: 72
  outliers final: 34
  residues processed: 182
  average time/residue: 0.4705
  time to fit residues: 94.2808
Evaluate side-chains
  152 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 112
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue   99 GLU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  801 SER
Chi-restraints excluded: chain A residue  838 GLN
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  629 ILE
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  711 THR
Chi-restraints excluded: chain C residue  744 SER
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  838 GLN
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue    9 LYS
Chi-restraints excluded: chain G residue   73 GLU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  149 VAL
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  711 THR
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  791 LEU
Chi-restraints excluded: chain G residue  801 SER
Chi-restraints excluded: chain G residue  838 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 143 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 24 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 66 optimal weight:    9.9990
   chunk 135 optimal weight:    0.9980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
A 234 GLN
A 625 GLN
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.187769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.116847 restraints weight = 13324.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.59
r_work: 0.3235 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.0842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11565  Z= 0.181
  Angle     :  0.594   6.284  15750  Z= 0.314
  Chirality :  0.048   0.235   1728
  Planarity :  0.004   0.046   2097
  Dihedral  :  5.995  52.496   1643
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  5.87 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 22.00 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.13 (0.21), residues: 1464
  helix:  0.55 (0.52), residues: 108
  sheet:  0.91 (0.20), residues: 564
  loop : -0.95 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 121 
 TYR   0.010   0.002   TYR G 685 
 PHE   0.014   0.002   PHE A 773 
 TRP   0.015   0.002   TRP C 807 
 HIS   0.001   0.000   HIS C 780 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.18 (11565)
  covalent geometry    : angle       0.59410 /  0.31 (15750)
  hydrogen bonds       : bond        0.03495 /  2.35 (  415)
  hydrogen bonds       : angle       5.60380 /  3.89 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 123
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ARG cc_start: 0.7342 (mtm110) cc_final: 0.7000 (mtm180)
REVERT: A  837 GLN cc_start: 0.6314 (mm110) cc_final: 0.5814 (mp-120)
REVERT: A  838 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6298 (tm-30)
REVERT: A  847 GLN cc_start: 0.7313 (tt0) cc_final: 0.6927 (tt0)
REVERT: C  190 ARG cc_start: 0.7427 (mtm110) cc_final: 0.7135 (mtm180)
REVERT: C  838 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.6259 (tm-30)
REVERT: G    9 LYS cc_start: 0.4376 (OUTLIER) cc_final: 0.3649 (pptt)
REVERT: G   59 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7437 (mp)
REVERT: G   91 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6685 (mt-10)
REVERT: G  700 GLU cc_start: 0.7202 (pm20) cc_final: 0.6995 (pm20)
REVERT: G  838 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6010 (tm-30)
REVERT: G  855 LYS cc_start: 0.4667 (OUTLIER) cc_final: 0.4057 (tttm)
  outliers start: 82
  outliers final: 40
  residues processed: 190
  average time/residue: 0.4779
  time to fit residues: 99.2937
Evaluate side-chains
  157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 110
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  801 SER
Chi-restraints excluded: chain A residue  838 GLN
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  629 ILE
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  711 THR
Chi-restraints excluded: chain C residue  744 SER
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  838 GLN
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue    9 LYS
Chi-restraints excluded: chain G residue   59 LEU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  149 VAL
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  211 THR
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  711 THR
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  791 LEU
Chi-restraints excluded: chain G residue  801 SER
Chi-restraints excluded: chain G residue  838 GLN
Chi-restraints excluded: chain G residue  848 VAL
Chi-restraints excluded: chain G residue  855 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
A 625 GLN
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.187798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.116555 restraints weight = 13395.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.60
r_work: 0.3294 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3183 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.0986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11565  Z= 0.178
  Angle     :  0.593   6.585  15750  Z= 0.312
  Chirality :  0.048   0.268   1728
  Planarity :  0.004   0.042   2097
  Dihedral  :  5.997  53.835   1643
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.15 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 22.08 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.15 (0.22), residues: 1464
  helix:  0.53 (0.52), residues: 108
  sheet:  0.91 (0.20), residues: 564
  loop : -0.97 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 121 
 TYR   0.011   0.002   TYR G 685 
 PHE   0.013   0.002   PHE A 773 
 TRP   0.015   0.002   TRP C 807 
 HIS   0.001   0.000   HIS C 780 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00404 /  0.18 (11565)
  covalent geometry    : angle       0.59261 /  0.31 (15750)
  hydrogen bonds       : bond        0.03328 /  2.24 (  415)
  hydrogen bonds       : angle       5.51236 /  3.83 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 112
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.7408 (mtm110) cc_final: 0.7059 (mtm180)
REVERT: A  838 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6350 (tm-30)
REVERT: G    9 LYS cc_start: 0.4606 (OUTLIER) cc_final: 0.3754 (pptt)
REVERT: G   91 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6697 (mt-10)
REVERT: G  700 GLU cc_start: 0.7153 (pm20) cc_final: 0.6915 (pm20)
REVERT: G  838 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6057 (tm-30)
REVERT: G  855 LYS cc_start: 0.4720 (OUTLIER) cc_final: 0.4091 (tttm)
  outliers start: 82
  outliers final: 44
  residues processed: 179
  average time/residue: 0.4500
  time to fit residues: 88.7828
Evaluate side-chains
  154 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 105
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  801 SER
Chi-restraints excluded: chain A residue  838 GLN
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  711 THR
Chi-restraints excluded: chain C residue  744 SER
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue    9 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  149 VAL
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  211 THR
Chi-restraints excluded: chain G residue  241 ILE
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  711 THR
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  791 LEU
Chi-restraints excluded: chain G residue  801 SER
Chi-restraints excluded: chain G residue  838 GLN
Chi-restraints excluded: chain G residue  848 VAL
Chi-restraints excluded: chain G residue  855 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 146 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 114 optimal weight:    0.0050
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.6394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
A 625 GLN
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.189281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.118765 restraints weight = 13277.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 2.59
r_work: 0.3314 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11565  Z= 0.117
  Angle     :  0.543   6.085  15750  Z= 0.285
  Chirality :  0.046   0.233   1728
  Planarity :  0.004   0.047   2097
  Dihedral  :  5.603  58.669   1641
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.71 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 23.60 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.02 (0.22), residues: 1464
  helix:  0.72 (0.52), residues: 108
  sheet:  0.99 (0.21), residues: 564
  loop : -0.90 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 121 
 TYR   0.008   0.001   TYR C 685 
 PHE   0.011   0.001   PHE A 235 
 TRP   0.010   0.001   TRP G 739 
 HIS   0.001   0.000   HIS C   8 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 (11565)
  covalent geometry    : angle       0.54275 /  0.29 (15750)
  hydrogen bonds       : bond        0.02846 /  1.92 (  415)
  hydrogen bonds       : angle       5.22559 /  3.64 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 115
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.7422 (mtm110) cc_final: 0.7060 (mtm180)
REVERT: G  700 GLU cc_start: 0.7130 (pm20) cc_final: 0.6832 (pm20)
  outliers start: 62
  outliers final: 27
  residues processed: 170
  average time/residue: 0.4393
  time to fit residues: 82.1893
Evaluate side-chains
  135 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  744 SER
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain G residue  149 VAL
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  211 THR
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  848 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 130 optimal weight:    0.8980
   chunk 95 optimal weight:    0.3980
   chunk 131 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0030
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:    8.9990
   chunk 114 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 141 optimal weight:    0.4980
   overall best weight:    0.5390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
A 625 GLN
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.189841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.119648 restraints weight = 13245.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 2.58
r_work: 0.3321 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.1165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11565  Z= 0.112
  Angle     :  0.543   7.124  15750  Z= 0.285
  Chirality :  0.046   0.305   1728
  Planarity :  0.004   0.039   2097
  Dihedral  :  5.130  59.497   1632
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.92 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 23.69 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.05 (0.22), residues: 1464
  helix:  0.89 (0.52), residues: 108
  sheet:  0.95 (0.21), residues: 570
  loop : -0.81 (0.22), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G 121 
 TYR   0.007   0.001   TYR G 685 
 PHE   0.011   0.001   PHE A 235 
 TRP   0.010   0.001   TRP G 739 
 HIS   0.001   0.000   HIS C 780 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 (11565)
  covalent geometry    : angle       0.54273 /  0.28 (15750)
  hydrogen bonds       : bond        0.02727 /  1.84 (  415)
  hydrogen bonds       : angle       5.11235 /  3.56 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 114
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 GLU cc_start: 0.7129 (pm20) cc_final: 0.6780 (pt0)
REVERT: A  190 ARG cc_start: 0.7386 (mtm110) cc_final: 0.7035 (mtm180)
REVERT: A  838 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6295 (tm-30)
REVERT: C  132 GLU cc_start: 0.7314 (pm20) cc_final: 0.6907 (pt0)
REVERT: G    9 LYS cc_start: 0.4455 (OUTLIER) cc_final: 0.3706 (pptt)
REVERT: G  119 ARG cc_start: 0.6333 (mtm110) cc_final: 0.6052 (mtm-85)
REVERT: G  700 GLU cc_start: 0.7078 (pm20) cc_final: 0.6719 (pm20)
REVERT: G  838 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.5999 (tm-30)
  outliers start: 56
  outliers final: 36
  residues processed: 161
  average time/residue: 0.4887
  time to fit residues: 86.3224
Evaluate side-chains
  150 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 111
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  801 SER
Chi-restraints excluded: chain A residue  838 GLN
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  639 LEU
Chi-restraints excluded: chain C residue  744 SER
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue    9 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain G residue  149 VAL
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  801 SER
Chi-restraints excluded: chain G residue  838 GLN
Chi-restraints excluded: chain G residue  848 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0050
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    2.9990
   chunk 122 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0050
   chunk 17 optimal weight:    9.9990
   chunk 109 optimal weight:   10.0000
   chunk 136 optimal weight:    2.9990
   overall best weight:    0.7012

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.189675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.119400 restraints weight = 13294.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.58
r_work: 0.3317 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11565  Z= 0.122
  Angle     :  0.552   7.425  15750  Z= 0.289
  Chirality :  0.046   0.266   1728
  Planarity :  0.004   0.036   2097
  Dihedral  :  5.001  57.339   1630
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.64 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 23.60 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.08 (0.22), residues: 1464
  helix:  0.95 (0.52), residues: 108
  sheet:  1.09 (0.21), residues: 558
  loop : -0.87 (0.22), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 121 
 TYR   0.008   0.001   TYR G 685 
 PHE   0.011   0.001   PHE C 230 
 TRP   0.011   0.001   TRP C 807 
 HIS   0.001   0.000   HIS C 780 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 (11565)
  covalent geometry    : angle       0.55163 /  0.29 (15750)
  hydrogen bonds       : bond        0.02767 /  1.87 (  415)
  hydrogen bonds       : angle       5.13246 /  3.57 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 116
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A  132 GLU cc_start: 0.7080 (pm20) cc_final: 0.6716 (pt0)
REVERT: A  190 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6987 (mtm180)
REVERT: G    9 LYS cc_start: 0.4395 (OUTLIER) cc_final: 0.3524 (tptt)
REVERT: G   91 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6691 (mt-10)
REVERT: G  119 ARG cc_start: 0.6346 (mtm110) cc_final: 0.6055 (mtm-85)
REVERT: G  121 ARG cc_start: 0.7251 (ttp80) cc_final: 0.6640 (ttp80)
REVERT: G  700 GLU cc_start: 0.7109 (pm20) cc_final: 0.6761 (pm20)
REVERT: G  838 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.5996 (tm-30)
  outliers start: 60
  outliers final: 41
  residues processed: 167
  average time/residue: 0.4725
  time to fit residues: 87.0428
Evaluate side-chains
  155 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 111
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  123 SER
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  801 SER
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   32 LYS
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  177 ASP
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  241 ILE
Chi-restraints excluded: chain C residue  629 ILE
Chi-restraints excluded: chain C residue  639 LEU
Chi-restraints excluded: chain C residue  744 SER
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue    9 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  146 ASP
Chi-restraints excluded: chain G residue  149 VAL
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  211 THR
Chi-restraints excluded: chain G residue  241 ILE
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  801 SER
Chi-restraints excluded: chain G residue  838 GLN
Chi-restraints excluded: chain G residue  848 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.0040
   chunk 81 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0170
   chunk 62 optimal weight:    0.8980
   chunk 142 optimal weight:    2.9990
   chunk 79 optimal weight:    0.2980
   chunk 98 optimal weight:   10.0000
   overall best weight:    0.4230

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
A 131 GLN
A 625 GLN
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.190849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.120847 restraints weight = 13284.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 2.58
r_work: 0.3339 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11565  Z= 0.102
  Angle     :  0.532   7.176  15750  Z= 0.279
  Chirality :  0.046   0.237   1728
  Planarity :  0.003   0.038   2097
  Dihedral  :  4.811  51.519   1630
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.58 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 24.70 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.18 (0.22), residues: 1464
  helix:  1.13 (0.52), residues: 108
  sheet:  0.91 (0.21), residues: 585
  loop : -0.65 (0.23), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 121 
 TYR   0.007   0.001   TYR G 751 
 PHE   0.012   0.001   PHE A 235 
 TRP   0.009   0.001   TRP G 739 
 HIS   0.001   0.000   HIS C 780 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00214 /  0.10 (11565)
  covalent geometry    : angle       0.53249 /  0.28 (15750)
  hydrogen bonds       : bond        0.02535 /  1.71 (  415)
  hydrogen bonds       : angle       4.99039 /  3.48 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 114
  time to evaluate  : 0.449 
Fit side-chains
REVERT: A  132 GLU cc_start: 0.7161 (pm20) cc_final: 0.6770 (pt0)
REVERT: A  169 ARG cc_start: 0.7896 (ttp-170) cc_final: 0.7486 (ttp-170)
REVERT: A  171 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7096 (mt-10)
REVERT: A  190 ARG cc_start: 0.7332 (mtm110) cc_final: 0.7012 (mtm180)
REVERT: A  234 GLN cc_start: 0.6671 (pt0) cc_final: 0.6320 (tt0)
REVERT: A  838 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6344 (tm-30)
REVERT: C    9 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.4463 (tptt)
REVERT: C  132 GLU cc_start: 0.7299 (pm20) cc_final: 0.6909 (pt0)
REVERT: C  190 ARG cc_start: 0.7329 (mtm110) cc_final: 0.6762 (mtm180)
REVERT: C  236 GLN cc_start: 0.8179 (tt0) cc_final: 0.7848 (tt0)
REVERT: G    9 LYS cc_start: 0.4465 (OUTLIER) cc_final: 0.3590 (tptt)
REVERT: G   59 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7434 (mt)
REVERT: G  119 ARG cc_start: 0.6369 (mtm110) cc_final: 0.6096 (mtm-85)
REVERT: G  121 ARG cc_start: 0.7292 (ttp80) cc_final: 0.6690 (ttp80)
REVERT: G  190 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7038 (mtm180)
REVERT: G  195 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7326 (m110)
REVERT: G  700 GLU cc_start: 0.7062 (pm20) cc_final: 0.6692 (pm20)
REVERT: G  838 GLN cc_start: 0.6739 (OUTLIER) cc_final: 0.6023 (tm-30)
REVERT: G  846 MET cc_start: 0.6640 (mtm) cc_final: 0.6311 (ttt)
  outliers start: 49
  outliers final: 27
  residues processed: 155
  average time/residue: 0.5261
  time to fit residues: 88.9425
Evaluate side-chains
  138 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  801 SER
Chi-restraints excluded: chain A residue  838 GLN
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue    9 LYS
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  857 VAL
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue    9 LYS
Chi-restraints excluded: chain G residue   59 LEU
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  195 ASN
Chi-restraints excluded: chain G residue  211 THR
Chi-restraints excluded: chain G residue  241 ILE
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  838 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 129 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 96 optimal weight:    0.1980
   chunk 16 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 123 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   overall best weight:    1.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
A 234 GLN
A 625 GLN
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.188162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.117206 restraints weight = 13146.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.58
r_work: 0.3296 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11565  Z= 0.208
  Angle     :  0.607   6.912  15750  Z= 0.318
  Chirality :  0.048   0.239   1728
  Planarity :  0.004   0.050   2097
  Dihedral  :  5.273  53.386   1630
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.08 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.21 %
    Favored  : 70.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.02 (0.22), residues: 1464
  helix:  0.90 (0.52), residues: 108
  sheet:  1.06 (0.21), residues: 558
  loop : -0.91 (0.22), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 169 
 TYR   0.011   0.002   TYR C 685 
 PHE   0.015   0.002   PHE A 773 
 TRP   0.016   0.002   TRP C 807 
 HIS   0.001   0.000   HIS G 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00478 /  0.21 (11565)
  covalent geometry    : angle       0.60744 /  0.32 (15750)
  hydrogen bonds       : bond        0.03263 /  2.21 (  415)
  hydrogen bonds       : angle       5.37892 /  3.73 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 108
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: A  190 ARG cc_start: 0.7342 (mtm110) cc_final: 0.6948 (mtm180)
REVERT: A  837 GLN cc_start: 0.6316 (mm110) cc_final: 0.5839 (mp-120)
REVERT: A  838 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6395 (tm-30)
REVERT: A  847 GLN cc_start: 0.7289 (tt0) cc_final: 0.6901 (tt0)
REVERT: C    9 LYS cc_start: 0.5377 (OUTLIER) cc_final: 0.4450 (tptp)
REVERT: C  190 ARG cc_start: 0.7413 (mtm110) cc_final: 0.6752 (mtm180)
REVERT: G    9 LYS cc_start: 0.4914 (OUTLIER) cc_final: 0.3862 (tptp)
REVERT: G  121 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6755 (ttp80)
REVERT: G  838 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6149 (tm-30)
  outliers start: 49
  outliers final: 32
  residues processed: 147
  average time/residue: 0.4428
  time to fit residues: 72.2104
Evaluate side-chains
  141 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 105
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  801 SER
Chi-restraints excluded: chain A residue  838 GLN
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue    9 LYS
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  123 SER
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  744 SER
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue    9 LYS
Chi-restraints excluded: chain G residue  149 VAL
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  211 THR
Chi-restraints excluded: chain G residue  241 ILE
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  801 SER
Chi-restraints excluded: chain G residue  838 GLN
Chi-restraints excluded: chain G residue  848 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 106 optimal weight:    0.0470
   chunk 127 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0870
   chunk 61 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.4456

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
C  83 HIS
C 234 GLN
G  83 HIS
G 625 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.190179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.119884 restraints weight = 13295.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.58
r_work: 0.3326 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  11565  Z= 0.107
  Angle     :  0.542   7.795  15750  Z= 0.284
  Chirality :  0.046   0.231   1728
  Planarity :  0.004   0.045   2097
  Dihedral  :  4.922  49.936   1630
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  4.51 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 26.48 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.12 (0.22), residues: 1464
  helix:  1.08 (0.52), residues: 108
  sheet:  0.86 (0.21), residues: 585
  loop : -0.69 (0.23), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 169 
 TYR   0.007   0.001   TYR C 685 
 PHE   0.011   0.001   PHE C 230 
 TRP   0.009   0.001   TRP G 739 
 HIS   0.001   0.000   HIS C 780 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00227 /  0.11 (11565)
  covalent geometry    : angle       0.54154 /  0.28 (15750)
  hydrogen bonds       : bond        0.02619 /  1.77 (  415)
  hydrogen bonds       : angle       5.07214 /  3.53 ( 1170)

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

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

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2928 Ramachandran restraints generated.
    1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 110
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A  190 ARG cc_start: 0.7314 (mtm110) cc_final: 0.6952 (mtm180)
REVERT: A  699 MET cc_start: 0.7518 (mmp) cc_final: 0.7208 (mmm)
REVERT: A  700 GLU cc_start: 0.7309 (pm20) cc_final: 0.6908 (pm20)
REVERT: A  837 GLN cc_start: 0.6203 (mm110) cc_final: 0.5729 (mp-120)
REVERT: A  838 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6344 (tm-30)
REVERT: C    9 LYS cc_start: 0.5301 (OUTLIER) cc_final: 0.4301 (tmtt)
REVERT: C  132 GLU cc_start: 0.7309 (pm20) cc_final: 0.6906 (pt0)
REVERT: C  190 ARG cc_start: 0.7337 (mtm110) cc_final: 0.6682 (mtm180)
REVERT: G    9 LYS cc_start: 0.4696 (OUTLIER) cc_final: 0.3726 (tptp)
REVERT: G   91 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6708 (mt-10)
REVERT: G  119 ARG cc_start: 0.6356 (mtm110) cc_final: 0.6077 (mtm-85)
REVERT: G  190 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7037 (mtm180)
REVERT: G  838 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6039 (tm-30)
REVERT: G  846 MET cc_start: 0.6706 (mtm) cc_final: 0.6262 (ttt)
  outliers start: 38
  outliers final: 27
  residues processed: 142
  average time/residue: 0.4828
  time to fit residues: 75.3708
Evaluate side-chains
  139 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 107
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  146 ASP
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  717 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  782 VAL
Chi-restraints excluded: chain A residue  801 SER
Chi-restraints excluded: chain A residue  838 GLN
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain C residue    6 THR
Chi-restraints excluded: chain C residue    9 LYS
Chi-restraints excluded: chain C residue   17 GLN
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain C residue  168 SER
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  766 THR
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain G residue    6 THR
Chi-restraints excluded: chain G residue    9 LYS
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  168 SER
Chi-restraints excluded: chain G residue  211 THR
Chi-restraints excluded: chain G residue  629 ILE
Chi-restraints excluded: chain G residue  644 LEU
Chi-restraints excluded: chain G residue  717 THR
Chi-restraints excluded: chain G residue  766 THR
Chi-restraints excluded: chain G residue  801 SER
Chi-restraints excluded: chain G residue  838 GLN
Chi-restraints excluded: chain G residue  848 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 107 optimal weight:    4.9990
   chunk 117 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  83 HIS
C  83 HIS
C 234 GLN
G  83 HIS
G 236 GLN
G 625 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.187943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.118289 restraints weight = 13326.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.53
r_work: 0.3299 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  11565  Z= 0.241
  Angle     :  0.637   7.358  15750  Z= 0.334
  Chirality :  0.049   0.239   1728
  Planarity :  0.005   0.050   2097
  Dihedral  :  5.458  53.624   1630
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  6.22 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.89 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.09 (0.22), residues: 1464
  helix:  0.80 (0.52), residues: 108
  sheet:  0.91 (0.21), residues: 564
  loop : -0.93 (0.22), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 169 
 TYR   0.012   0.002   TYR A 170 
 PHE   0.017   0.002   PHE A 773 
 TRP   0.017   0.002   TRP C 807 
 HIS   0.001   0.000   HIS G 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00559 /  0.24 (11565)
  covalent geometry    : angle       0.63743 /  0.33 (15750)
  hydrogen bonds       : bond        0.03524 /  2.38 (  415)
  hydrogen bonds       : angle       5.52726 /  3.84 ( 1170)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5443.77 seconds
wall clock time: 93 minutes 1.32 seconds (5581.32 seconds total)