Starting phenix.real_space_refine
on Wed Mar  4 02:19:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uph_20839/03_2026/6uph_20839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uph_20839/03_2026/6uph_20839.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uph_20839/03_2026/6uph_20839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uph_20839/03_2026/6uph_20839.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uph_20839/03_2026/6uph_20839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uph_20839/03_2026/6uph_20839.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.033 sd=   0.037
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     238      5.49       5
     S      10      5.16       5
     C    5969      2.51       5
     N    1975      2.21       5
     O    2485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10677
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 766
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 766
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 1, 'TRANS': 91}
    Chain: "B"
      Number of atoms: 630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 630
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 744
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "D"
      Number of atoms: 752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 752
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 794
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 630
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 630
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 762
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 762
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "H"
      Number of atoms: 720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 720
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 2424
          Classifications: {'DNA': 119}
          Link IDs: {'rna3p': 118}
    Chain: "J"
      Number of atoms: 2455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 2455
          Classifications: {'DNA': 119}
          Link IDs: {'rna3p': 118}
  Time building chain proxies: 2.53, per 1000 atoms: 0.24
  Number of scatterers: 10677
  At special positions: 0
  Unit cell: (119.709, 105.276, 118.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     238     15.00
     O    2485      8.00
     N    1975      7.00
     C    5969      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 323.6 milliseconds
  

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      71.6% alpha, 3.3% beta
      83 base pairs and 211 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 136 through 146
      removed outlier: 3.538A  pdb=" N   ILE A 142 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 167
      removed outlier: 3.715A  pdb=" N   ASP A 167 " --> pdb=" O   LYS A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 207
      removed outlier: 3.576A  pdb=" N   ILE A 183 " --> pdb=" O   GLN A 179 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   MET A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY A 196 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   HIS A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 226
      removed outlier: 3.546A  pdb=" N   MET A 218 " --> pdb=" O   MET A 214 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG A 222 " --> pdb=" O   MET A 218 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG A 223 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 30
      removed outlier: 3.611A  pdb=" N   ILE B  30 " --> pdb=" O   ILE B  27 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 43
    Processing helix  chain 'B' and resid 50 through 77
      removed outlier: 3.751A  pdb=" N   GLU B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ARG B  56 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ASP B  69 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA B  77 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 93
      removed outlier: 3.665A  pdb=" N   VAL B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL B  88 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 23
      removed outlier: 3.797A  pdb=" N   ALA C  22 " --> pdb=" O   ARG C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 37
      removed outlier: 3.576A  pdb=" N   VAL C  31 " --> pdb=" O   PRO C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 74
      removed outlier: 3.604A  pdb=" N   ALA C  71 " --> pdb=" O   ALA C  67 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   ASN C  74 " --> pdb=" O   ALA C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 90
      removed outlier: 3.615A  pdb=" N   LEU C  84 " --> pdb=" O   ILE C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'D' and resid 42 through 54
      removed outlier: 3.780A  pdb=" N   LYS D  48 " --> pdb=" O   SER D  44 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   THR D  53 " --> pdb=" O   VAL D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 88
      removed outlier: 3.518A  pdb=" N   LYS D  84 " --> pdb=" O   THR D  80 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA D  87 " --> pdb=" O   SER D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 95 through 107
    Processing helix  chain 'D' and resid 109 through 127
      removed outlier: 3.590A  pdb=" N   LYS D 113 " --> pdb=" O   GLY D 109 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   HIS D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL D 116 " --> pdb=" O   ALA D 112 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER D 117 " --> pdb=" O   LYS D 113 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL D 123 " --> pdb=" O   GLY D 119 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 134 through 146
      removed outlier: 3.886A  pdb=" N   ALA E 138 " --> pdb=" O   PRO E 134 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 167
      removed outlier: 3.512A  pdb=" N   PHE E 158 " --> pdb=" O   SER E 154 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASP E 167 " --> pdb=" O   LYS E 163 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 208
      removed outlier: 3.681A  pdb=" N   MET E 184 " --> pdb=" O   SER E 180 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   HIS E 200 " --> pdb=" O   GLY E 196 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA E 208 " --> pdb=" O   LEU E 204 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 214 through 225
      removed outlier: 3.699A  pdb=" N   MET E 218 " --> pdb=" O   MET E 214 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU E 220 " --> pdb=" O   LYS E 216 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 26 through 30
    Processing helix  chain 'F' and resid 31 through 41
      removed outlier: 3.535A  pdb=" N   ARG F  37 " --> pdb=" O   PRO F  33 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU F  38 " --> pdb=" O   ALA F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 77
      removed outlier: 4.043A  pdb=" N   GLU F  54 " --> pdb=" O   LEU F  50 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ASP F  69 " --> pdb=" O   SER F  65 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   THR F  72 " --> pdb=" O   ARG F  68 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA F  77 " --> pdb=" O   TYR F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 93
      removed outlier: 3.759A  pdb=" N   VAL F  87 " --> pdb=" O   THR F  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 23
      removed outlier: 3.802A  pdb=" N   ALA G  22 " --> pdb=" O   ARG G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 37
      removed outlier: 3.532A  pdb=" N   VAL G  31 " --> pdb=" O   PRO G  27 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG G  33 " --> pdb=" O   GLY G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 47 through 72
    Processing helix  chain 'G' and resid 80 through 89
      removed outlier: 3.680A  pdb=" N   LEU G  84 " --> pdb=" O   ILE G  80 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 98
      removed outlier: 3.556A  pdb=" N   LEU G  98 " --> pdb=" O   LEU G  94 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 42 through 54
      removed outlier: 3.742A  pdb=" N   LYS H  48 " --> pdb=" O   SER H  44 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LYS H  51 " --> pdb=" O   TYR H  47 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   THR H  53 " --> pdb=" O   VAL H  49 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 60 through 89
      removed outlier: 3.506A  pdb=" N   ASN H  72 " --> pdb=" O   ASN H  68 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU H  76 " --> pdb=" O   ASN H  72 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LYS H  84 " --> pdb=" O   THR H  80 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA H  87 " --> pdb=" O   SER H  83 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 95 through 107
    Processing helix  chain 'H' and resid 108 through 127
      removed outlier: 3.684A  pdb=" N   HIS H 114 " --> pdb=" O   GLU H 110 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER H 117 " --> pdb=" O   LYS H 113 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178
      removed outlier: 6.839A  pdb=" N   ARG A 177 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 213
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.135A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103
      removed outlier: 6.711A  pdb=" N   THR C 102 " --> pdb=" O   TYR F  99 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 177 through 178
      removed outlier: 6.708A  pdb=" N   ARG E 177 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.078A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  94 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79

    335 hydrogen bonds defined for protein.
    996 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      203 hydrogen bonds
      398 hydrogen bond angles
      0 basepair planarities
      83 basepair parallelities
      211 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1727
        1.33 -     1.45: 3818
        1.45 -     1.57: 5306
        1.57 -     1.68: 474
        1.68 -     1.80: 20
  Bond restraints: 11345
  Sorted by residual:
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.01e+00
  bond pdb=" CB  ASN H  72 "
       pdb=" CG  ASN H  72 "
    ideal  model  delta    sigma   weight residual
    1.516  1.486  0.030 2.50e-02 1.60e+03 1.44e+00
  bond pdb=" CG  PRO C  49 "
       pdb=" CD  PRO C  49 "
    ideal  model  delta    sigma   weight residual
    1.503  1.463  0.040 3.40e-02 8.65e+02 1.38e+00
  bond pdb=" CG1 ILE D 106 "
       pdb=" CD1 ILE D 106 "
    ideal  model  delta    sigma   weight residual
    1.513  1.468  0.045 3.90e-02 6.57e+02 1.30e+00
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.26e+00
  ... (remaining 11340 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 15652
        1.55 -     3.09: 651
        3.09 -     4.64: 33
        4.64 -     6.18: 4
        6.18 -     7.73: 2
  Bond angle restraints: 16342
  Sorted by residual:
  angle pdb=" N   GLY H 109 "
        pdb=" CA  GLY H 109 "
        pdb=" C   GLY H 109 "
      ideal   model   delta    sigma   weight residual
     113.18  120.91   -7.73 2.37e+00 1.78e-01 1.06e+01
  angle pdb=" C3'  DT J   5 "
        pdb=" C2'  DT J   5 "
        pdb=" C1'  DT J   5 "
      ideal   model   delta    sigma   weight residual
     101.60   97.98    3.62 1.50e+00 4.44e-01 5.81e+00
  angle pdb=" C3'  DT J -17 "
        pdb=" O3'  DT J -17 "
        pdb=" P    DT J -16 "
      ideal   model   delta    sigma   weight residual
     120.20  123.64   -3.44 1.50e+00 4.44e-01 5.27e+00
  angle pdb=" C3'  DG J  20 "
        pdb=" O3'  DG J  20 "
        pdb=" P    DG J  21 "
      ideal   model   delta    sigma   weight residual
     120.20  123.64   -3.44 1.50e+00 4.44e-01 5.25e+00
  angle pdb=" N   GLY D 109 "
        pdb=" CA  GLY D 109 "
        pdb=" C   GLY D 109 "
      ideal   model   delta    sigma   weight residual
     110.77  114.99   -4.22 1.93e+00 2.68e-01 4.79e+00
  ... (remaining 16337 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.93: 5127
       34.93 -    69.86: 1057
       69.86 -   104.78: 13
      104.78 -   139.71: 0
      139.71 -   174.64: 2
  Dihedral angle restraints: 6199
    sinusoidal: 4069
      harmonic: 2130
  Sorted by residual:
  dihedral pdb=" CA  PRO H 108 "
           pdb=" C   PRO H 108 "
           pdb=" N   GLY H 109 "
           pdb=" CA  GLY H 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.17  -21.83     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  PRO D 108 "
           pdb=" C   PRO D 108 "
           pdb=" N   GLY D 109 "
           pdb=" CA  GLY D 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.30   20.70     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   45.36  174.64     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 6196 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 867
       0.027 -    0.054: 679
       0.054 -    0.081: 240
       0.081 -    0.108: 62
       0.108 -    0.135: 27
  Chirality restraints: 1875
  Sorted by residual:
  chirality pdb=" CA  PRO E 157 "
            pdb=" N   PRO E 157 "
            pdb=" C   PRO E 157 "
            pdb=" CB  PRO E 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CA  PRO C  81 "
            pdb=" N   PRO C  81 "
            pdb=" C   PRO C  81 "
            pdb=" CB  PRO C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  ASN H  72 "
            pdb=" N   ASN H  72 "
            pdb=" C   ASN H  72 "
            pdb=" CB  ASN H  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 1872 not shown)

  Planarity restraints: 1234
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 156 "    0.034 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO E 157 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO E 157 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E 157 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  32 "   -0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO B  33 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B  33 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  33 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 109 "    0.029 5.00e-02 4.00e+02   4.46e-02 3.18e+00
        pdb=" N   PRO C 110 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO C 110 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 110 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1231 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1468
        2.75 -     3.29: 8276
        3.29 -     3.83: 17618
        3.83 -     4.36: 25111
        4.36 -     4.90: 34893
  Nonbonded interactions: 87366
  Sorted by model distance:
  nonbonded pdb=" N4   DC I  51 "
            pdb=" O6   DG J -51 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O6   DG I  11 "
            pdb=" N4   DC J -11 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" OH  TYR B  99 "
            pdb=" OD2 ASP H  73 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O2   DC I -20 "
            pdb=" N2   DG J  20 "
     model   vdw
     2.274 2.496
  nonbonded pdb=" NZ  LYS E 215 "
            pdb=" OE1 GLN E 219 "
     model   vdw
     2.321 3.120
  ... (remaining 87361 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 136 through 228)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 17 through 113)
}
ncs_group {
  reference = (chain 'D' and resid 38 through 129)
  selection = chain 'H'
}

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:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.840
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:6.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
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      :  0.007   0.051  11345  Z= 0.327
  Angle     :  0.667   7.727  16342  Z= 0.400
  Chirality :  0.041   0.135   1875
  Planarity :  0.004   0.051   1234
  Dihedral  : 26.073 174.641   4823
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -5.67 (0.19), residues: 716
  helix: -3.90 (0.12), residues: 517
  sheet:  None (None), residues: 0
  loop : -2.57 (0.33), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  93 
 TYR   0.013   0.002   TYR A 145 
 PHE   0.014   0.002   PHE F  62 
 TRP   0.004   0.002   TRP E 178 
 HIS   0.003   0.001   HIS G 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00735 (11345)
  covalent geometry    : angle       0.66671 (16342)
  hydrogen bonds       : bond        0.34023 (  538)
  hydrogen bonds       : angle      10.11388 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.178 
Fit side-chains
REVERT: E  155 LYS cc_start: 0.8637 (mttp) cc_final: 0.8278 (mtpt)
REVERT: E  174 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6886 (mm110)
REVERT: G   16 GLN cc_start: 0.7204 (mt0) cc_final: 0.6986 (pm20)
REVERT: H   73 ASP cc_start: 0.8800 (t0) cc_final: 0.8453 (t0)
  outliers start: 0
  outliers final: 1
  residues processed: 142
  average time/residue: 1.0054
  time to fit residues: 148.7106
Evaluate side-chains
  130 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
B  76 HIS
H 100 GLN
H 114 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.159059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.133233 restraints weight = 12264.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 1.05
r_work: 0.3512 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  11345  Z= 0.181
  Angle     :  0.585   7.395  16342  Z= 0.352
  Chirality :  0.035   0.125   1875
  Planarity :  0.005   0.044   1234
  Dihedral  : 29.283 176.583   3395
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 10.99 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.27), residues: 716
  helix: -0.75 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop : -2.40 (0.31), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  72 
 TYR   0.015   0.001   TYR E 140 
 PHE   0.011   0.002   PHE F  62 
 TRP   0.002   0.001   TRP A 178 
 HIS   0.002   0.001   HIS B  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (11345)
  covalent geometry    : angle       0.58462 (16342)
  hydrogen bonds       : bond        0.07718 (  538)
  hydrogen bonds       : angle       3.18482 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7845 (mtm110)
REVERT: A  214 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8981 (mtt)
REVERT: C   92 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.8026 (m-30)
REVERT: C  109 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8554 (mp)
REVERT: D   76 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7777 (tt0)
REVERT: F   64 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8368 (mt-10)
REVERT: H   73 ASP cc_start: 0.8922 (t0) cc_final: 0.8568 (t70)
REVERT: H   76 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7851 (tm-30)
  outliers start: 11
  outliers final: 2
  residues processed: 145
  average time/residue: 0.9783
  time to fit residues: 148.1963
Evaluate side-chains
  138 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain F residue   64 GLU
Chi-restraints excluded: chain F residue   93 ARG
Chi-restraints excluded: chain H residue   76 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0970
   chunk 14 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
H  89 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.161017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.135320 restraints weight = 12425.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.05
r_work: 0.3539 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11345  Z= 0.156
  Angle     :  0.528   6.071  16342  Z= 0.320
  Chirality :  0.033   0.121   1875
  Planarity :  0.004   0.043   1234
  Dihedral  : 29.144 178.089   3391
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.28 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.31), residues: 716
  helix:  0.86 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -2.13 (0.33), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  93 
 TYR   0.014   0.001   TYR E 140 
 PHE   0.010   0.001   PHE F  62 
 TRP   0.002   0.001   TRP A 178 
 HIS   0.001   0.000   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (11345)
  covalent geometry    : angle       0.52845 (16342)
  hydrogen bonds       : bond        0.06291 (  538)
  hydrogen bonds       : angle       2.82597 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 137
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  141 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8100 (mt-10)
REVERT: A  143 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7808 (mtm110)
REVERT: C   74 ASN cc_start: 0.8301 (m-40) cc_final: 0.7985 (t0)
REVERT: C   92 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7921 (m-30)
REVERT: C  109 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8529 (mp)
REVERT: D   76 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7824 (tt0)
REVERT: E  174 GLN cc_start: 0.7478 (mm-40) cc_final: 0.6943 (mm-40)
REVERT: F   60 LYS cc_start: 0.9021 (tppp) cc_final: 0.8735 (tttp)
REVERT: G   16 GLN cc_start: 0.7490 (mt0) cc_final: 0.6790 (pm20)
REVERT: G   96 LYS cc_start: 0.8928 (tttm) cc_final: 0.8693 (tttp)
REVERT: H   73 ASP cc_start: 0.8926 (t0) cc_final: 0.8089 (t70)
  outliers start: 10
  outliers final: 2
  residues processed: 140
  average time/residue: 0.9117
  time to fit residues: 133.5273
Evaluate side-chains
  135 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain G residue   63 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 82 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  94 GLN
G 105 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.160956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.135201 restraints weight = 12366.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 1.04
r_work: 0.3538 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11345  Z= 0.158
  Angle     :  0.524   6.310  16342  Z= 0.316
  Chirality :  0.033   0.123   1875
  Planarity :  0.003   0.040   1234
  Dihedral  : 29.144 179.367   3391
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.09 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.97 (0.31), residues: 716
  helix:  1.57 (0.24), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.91 (0.34), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  36 
 TYR   0.014   0.001   TYR E 140 
 PHE   0.011   0.001   PHE F  62 
 TRP   0.002   0.001   TRP A 178 
 HIS   0.002   0.000   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11345)
  covalent geometry    : angle       0.52419 (16342)
  hydrogen bonds       : bond        0.06119 (  538)
  hydrogen bonds       : angle       2.73667 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.272 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.8169 (m-40) cc_final: 0.7899 (t0)
REVERT: C   92 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7895 (m-30)
REVERT: C  109 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8509 (mp)
REVERT: D   76 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7798 (tt0)
REVERT: E  174 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6903 (mm-40)
REVERT: F   60 LYS cc_start: 0.8987 (tppp) cc_final: 0.8745 (tttp)
REVERT: G   16 GLN cc_start: 0.7473 (mt0) cc_final: 0.6589 (pm20)
REVERT: H   73 ASP cc_start: 0.8930 (t0) cc_final: 0.8536 (t70)
REVERT: H   76 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7861 (tm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 136
  average time/residue: 0.8930
  time to fit residues: 127.0437
Evaluate side-chains
  137 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain H residue   76 GLU
Chi-restraints excluded: chain H residue   84 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 50 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 22 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
H 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.153966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.127099 restraints weight = 11951.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 1.08
r_work: 0.3434 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  11345  Z= 0.253
  Angle     :  0.621   7.443  16342  Z= 0.367
  Chirality :  0.039   0.159   1875
  Planarity :  0.004   0.043   1234
  Dihedral  : 29.416 178.894   3391
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.09 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.79 (0.31), residues: 716
  helix:  1.45 (0.23), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.99 (0.33), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  40 
 TYR   0.020   0.002   TYR A 140 
 PHE   0.014   0.002   PHE B  62 
 TRP   0.004   0.001   TRP E 178 
 HIS   0.002   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 (11345)
  covalent geometry    : angle       0.62143 (16342)
  hydrogen bonds       : bond        0.08065 (  538)
  hydrogen bonds       : angle       3.03827 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.287 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.8247 (m-40) cc_final: 0.7961 (t0)
REVERT: C  109 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8597 (mp)
REVERT: E  174 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7004 (mm-40)
REVERT: E  199 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8242 (mt-10)
REVERT: E  214 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.7981 (mmt)
REVERT: F   60 LYS cc_start: 0.9034 (tppp) cc_final: 0.8772 (tttp)
REVERT: F   64 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8370 (mt-10)
REVERT: H   73 ASP cc_start: 0.8958 (t0) cc_final: 0.8639 (t0)
REVERT: H   76 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7847 (tm-30)
  outliers start: 17
  outliers final: 5
  residues processed: 137
  average time/residue: 0.8937
  time to fit residues: 128.0855
Evaluate side-chains
  138 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain E residue  199 GLU
Chi-restraints excluded: chain E residue  214 MET
Chi-restraints excluded: chain F residue   64 GLU
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain H residue   76 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 47 optimal weight:    0.6980
   chunk 12 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
B  94 GLN
G 105 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.154450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127588 restraints weight = 12092.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.07
r_work: 0.3441 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3327 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11345  Z= 0.216
  Angle     :  0.599   7.296  16342  Z= 0.357
  Chirality :  0.037   0.145   1875
  Planarity :  0.004   0.043   1234
  Dihedral  : 29.409 178.642   3391
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.05 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.84 (0.31), residues: 716
  helix:  1.51 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -2.04 (0.33), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  40 
 TYR   0.017   0.002   TYR A 140 
 PHE   0.013   0.002   PHE B  62 
 TRP   0.003   0.001   TRP A 178 
 HIS   0.002   0.000   HIS H 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (11345)
  covalent geometry    : angle       0.59901 (16342)
  hydrogen bonds       : bond        0.07719 (  538)
  hydrogen bonds       : angle       3.04201 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.297 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.8221 (m-40) cc_final: 0.7939 (t0)
REVERT: C  109 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8591 (mp)
REVERT: E  174 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7003 (mm-40)
REVERT: E  199 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8243 (mt-10)
REVERT: F   60 LYS cc_start: 0.9012 (tppp) cc_final: 0.8729 (tttp)
REVERT: F   64 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8371 (mt-10)
REVERT: H   73 ASP cc_start: 0.8954 (t0) cc_final: 0.8623 (t0)
REVERT: H   76 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7853 (tm-30)
  outliers start: 15
  outliers final: 6
  residues processed: 134
  average time/residue: 0.9171
  time to fit residues: 128.6371
Evaluate side-chains
  138 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain E residue  199 GLU
Chi-restraints excluded: chain F residue   64 GLU
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain H residue   76 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 68 optimal weight:   20.0000
   chunk 22 optimal weight:    0.0470
   chunk 32 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
G 105 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.157282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.130637 restraints weight = 12089.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 1.07
r_work: 0.3480 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3368 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11345  Z= 0.158
  Angle     :  0.554   6.545  16342  Z= 0.334
  Chirality :  0.033   0.133   1875
  Planarity :  0.003   0.038   1234
  Dihedral  : 29.348 178.718   3391
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.05 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.31), residues: 716
  helix:  1.84 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.89 (0.33), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 223 
 TYR   0.024   0.001   TYR A 140 
 PHE   0.010   0.001   PHE F  62 
 TRP   0.001   0.001   TRP A 178 
 HIS   0.002   0.000   HIS F  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (11345)
  covalent geometry    : angle       0.55425 (16342)
  hydrogen bonds       : bond        0.06439 (  538)
  hydrogen bonds       : angle       3.05637 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.346 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.8123 (m-40) cc_final: 0.7871 (t0)
REVERT: C   92 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7915 (m-30)
REVERT: C  109 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8558 (mp)
REVERT: D   76 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7762 (tt0)
REVERT: E  174 GLN cc_start: 0.7474 (mm-40) cc_final: 0.6727 (mt0)
REVERT: E  199 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8113 (mt-10)
REVERT: F   60 LYS cc_start: 0.8956 (tppp) cc_final: 0.8690 (tttp)
REVERT: G   16 GLN cc_start: 0.7443 (mt0) cc_final: 0.6769 (pm20)
REVERT: H   73 ASP cc_start: 0.8863 (t0) cc_final: 0.8433 (t0)
  outliers start: 13
  outliers final: 5
  residues processed: 136
  average time/residue: 0.9446
  time to fit residues: 134.4480
Evaluate side-chains
  138 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain E residue  199 GLU
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain H residue   84 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 40 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
H  89 ASN
H 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.158187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.131538 restraints weight = 12092.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 1.07
r_work: 0.3488 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11345  Z= 0.157
  Angle     :  0.540   7.146  16342  Z= 0.324
  Chirality :  0.033   0.124   1875
  Planarity :  0.003   0.041   1234
  Dihedral  : 29.230 179.712   3391
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.38 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.32), residues: 716
  helix:  2.14 (0.24), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.83 (0.33), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  36 
 TYR   0.022   0.001   TYR A 140 
 PHE   0.009   0.001   PHE F  62 
 TRP   0.003   0.001   TRP A 178 
 HIS   0.002   0.001   HIS C  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (11345)
  covalent geometry    : angle       0.54034 (16342)
  hydrogen bonds       : bond        0.06305 (  538)
  hydrogen bonds       : angle       2.81696 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.295 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.8077 (m-40) cc_final: 0.7833 (t0)
REVERT: C   92 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7931 (m-30)
REVERT: C  109 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8564 (mp)
REVERT: D   76 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7742 (tt0)
REVERT: E  174 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6908 (mm-40)
REVERT: E  199 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8226 (mt-10)
REVERT: F   60 LYS cc_start: 0.8980 (tppp) cc_final: 0.8725 (tttp)
REVERT: F   64 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8362 (mt-10)
REVERT: H   73 ASP cc_start: 0.8898 (t0) cc_final: 0.8476 (t0)
REVERT: H   89 ASN cc_start: 0.8284 (m110) cc_final: 0.8062 (m-40)
  outliers start: 12
  outliers final: 5
  residues processed: 133
  average time/residue: 0.9361
  time to fit residues: 130.4369
Evaluate side-chains
  139 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain E residue  199 GLU
Chi-restraints excluded: chain F residue   64 GLU
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain H residue   84 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0040
   chunk 15 optimal weight:    7.9990
   chunk 9 optimal weight:    0.3980
   chunk 5 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 68 optimal weight:   20.0000
   overall best weight:    3.2798

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

Flipped N/Q/H residues before XYZ refinement:
B  94 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.156155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.129482 restraints weight = 12063.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 1.06
r_work: 0.3465 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11345  Z= 0.194
  Angle     :  0.561   6.813  16342  Z= 0.335
  Chirality :  0.036   0.139   1875
  Planarity :  0.004   0.039   1234
  Dihedral  : 29.250 179.559   3391
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.54 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.31), residues: 716
  helix:  2.09 (0.23), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.85 (0.33), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG F  40 
 TYR   0.023   0.002   TYR A 140 
 PHE   0.011   0.002   PHE B  62 
 TRP   0.003   0.001   TRP A 178 
 HIS   0.002   0.000   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (11345)
  covalent geometry    : angle       0.56141 (16342)
  hydrogen bonds       : bond        0.06808 (  538)
  hydrogen bonds       : angle       2.83099 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.299 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.8105 (m-40) cc_final: 0.7866 (t0)
REVERT: C   92 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7936 (m-30)
REVERT: C  109 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8576 (mp)
REVERT: D   76 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7763 (tt0)
REVERT: E  174 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6717 (mt0)
REVERT: E  199 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8239 (mt-10)
REVERT: E  214 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8000 (mmt)
REVERT: F   60 LYS cc_start: 0.8991 (tppp) cc_final: 0.8739 (tttp)
REVERT: F   64 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8369 (mt-10)
REVERT: H   73 ASP cc_start: 0.8957 (t0) cc_final: 0.8642 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 133
  average time/residue: 0.9103
  time to fit residues: 126.8478
Evaluate side-chains
  139 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain E residue  199 GLU
Chi-restraints excluded: chain E residue  214 MET
Chi-restraints excluded: chain F residue   64 GLU
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain H residue   84 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   chunk 30 optimal weight:    4.9990
   chunk 89 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  94 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.156369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.129667 restraints weight = 12014.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 1.07
r_work: 0.3467 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11345  Z= 0.178
  Angle     :  0.557   6.660  16342  Z= 0.333
  Chirality :  0.035   0.135   1875
  Planarity :  0.004   0.039   1234
  Dihedral  : 29.251 179.519   3391
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.54 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.58 (0.31), residues: 716
  helix:  2.09 (0.23), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.85 (0.33), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  78 
 TYR   0.022   0.001   TYR A 140 
 PHE   0.011   0.001   PHE B  62 
 TRP   0.003   0.001   TRP A 178 
 HIS   0.001   0.000   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (11345)
  covalent geometry    : angle       0.55661 (16342)
  hydrogen bonds       : bond        0.06746 (  538)
  hydrogen bonds       : angle       2.82987 ( 1394)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.299 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.8103 (m-40) cc_final: 0.7865 (t0)
REVERT: C   92 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (m-30)
REVERT: C  109 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8575 (mp)
REVERT: D   76 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7760 (tt0)
REVERT: E  174 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6715 (mt0)
REVERT: E  199 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8231 (mt-10)
REVERT: E  214 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8000 (mmt)
REVERT: F   60 LYS cc_start: 0.8988 (tppp) cc_final: 0.8737 (tttp)
REVERT: F   64 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8364 (mt-10)
REVERT: H   73 ASP cc_start: 0.8952 (t0) cc_final: 0.8635 (t0)
  outliers start: 12
  outliers final: 5
  residues processed: 132
  average time/residue: 0.9310
  time to fit residues: 128.7620
Evaluate side-chains
  139 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 LYS
Chi-restraints excluded: chain C residue   92 ASP
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   76 GLU
Chi-restraints excluded: chain E residue  171 THR
Chi-restraints excluded: chain E residue  199 GLU
Chi-restraints excluded: chain E residue  214 MET
Chi-restraints excluded: chain F residue   64 GLU
Chi-restraints excluded: chain F residue   84 SER
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain H residue   84 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 85 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 65 optimal weight:   20.0000
   chunk 25 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 46 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    4.7786

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

Flipped N/Q/H residues before XYZ refinement:
B  94 GLN
H 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.154291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.127426 restraints weight = 12109.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3568 rms_B_bonded: 1.06
r_work: 0.3438 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11345  Z= 0.239
  Angle     :  0.609   7.361  16342  Z= 0.360
  Chirality :  0.038   0.155   1875
  Planarity :  0.004   0.039   1234
  Dihedral  : 29.371 178.991   3391
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 14.70 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.31), residues: 716
  helix:  1.84 (0.23), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.90 (0.33), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  41 
 TYR   0.023   0.002   TYR A 140 
 PHE   0.013   0.002   PHE B  62 
 TRP   0.003   0.001   TRP A 178 
 HIS   0.002   0.001   HIS G 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (11345)
  covalent geometry    : angle       0.60868 (16342)
  hydrogen bonds       : bond        0.07734 (  538)
  hydrogen bonds       : angle       2.96990 ( 1394)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4121.79 seconds
wall clock time: 70 minutes 33.41 seconds (4233.41 seconds total)