Starting phenix.real_space_refine
on Wed Feb  4 20:48:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rup_54273/02_2026/9rup_54273.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rup_54273/02_2026/9rup_54273.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rup_54273/02_2026/9rup_54273.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rup_54273/02_2026/9rup_54273.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rup_54273/02_2026/9rup_54273.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rup_54273/02_2026/9rup_54273.map"
  }
  resolution = 4.11
  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=   0.003 sd=   0.038
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      49      5.16       5
     C    8054      2.51       5
     N    2212      2.21       5
     O    2492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12807
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1551
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1916
          Classifications: {'peptide': 242}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 228}
    Chain: "E"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 829
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
    Chain: "C"
      Number of atoms: 2103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 260, 2103
          Classifications: {'peptide': 260}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 246}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 86
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 8}
    Chain: "a"
      Number of atoms: 1489
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1489
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 11, 'TRANS': 180}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "b"
      Number of atoms: 1765
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1765
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210}
          Chain breaks: 2
    Chain: "e"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 829
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
    Chain: "c"
      Number of atoms: 2153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2153
          Classifications: {'peptide': 265}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 251}
    Chain: "d"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 86
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 8}
  Time building chain proxies: 3.14, per 1000 atoms: 0.25
  Number of scatterers: 12807
  At special positions: 0
  Unit cell: (143.869, 130.724, 83.9845, 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      49     16.00
     O    2492      8.00
     N    2212      7.00
     C    8054      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  21 " - pdb=" SG  CYS B  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 143 " - pdb=" SG  CYS B 208 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  25 " - pdb=" SG  CYS E  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  99 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 201 " - pdb=" SG  CYS C 257 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a  22 " - pdb=" SG  CYS a  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  21 " - pdb=" SG  CYS b  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 143 " - pdb=" SG  CYS b 208 " distance=2.04
    Simple disulfide: pdb=" SG  CYS e  25 " - pdb=" SG  CYS e  80 " distance=2.03
    Simple disulfide: pdb=" SG  CYS c  99 " - pdb=" SG  CYS c 162 " distance=2.04
    Simple disulfide: pdb=" SG  CYS c 201 " - pdb=" SG  CYS c 257 " distance=2.03

  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: 1.05
  Conformation dependent library (CDL) restraints added in 579.0 milliseconds
  

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2992

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 32 sheets defined
      10.3% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'B' and resid 80 through 84
      removed outlier: 3.711A  pdb=" N   ASP B  83 " --> pdb=" O   GLU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 118
      removed outlier: 3.504A  pdb=" N   ASN B 117 " --> pdb=" O   ASP B 114 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   VAL B 118 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 114 through 118'
    Processing helix  chain 'B' and resid 130 through 135
      removed outlier: 4.688A  pdb=" N   HIS B 135 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.664A  pdb=" N   ASN B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 61
      removed outlier: 3.513A  pdb=" N   TRP C  58 " --> pdb=" O   GLY C  54 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 76
      removed outlier: 3.653A  pdb=" N   ARG C  73 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ALA C  74 " --> pdb=" O   GLN C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 83
      removed outlier: 3.617A  pdb=" N   TYR C  83 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 148
    Processing helix  chain 'C' and resid 149 through 160
    Processing helix  chain 'C' and resid 160 through 174
    Processing helix  chain 'b' and resid 80 through 84
      removed outlier: 3.635A  pdb=" N   ASP b  83 " --> pdb=" O   GLU b  80 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 195 through 201
    Processing helix  chain 'c' and resid 54 through 61
    Processing helix  chain 'c' and resid 64 through 76
      removed outlier: 5.173A  pdb=" N   GLN c  70 " --> pdb=" O   LYS c  66 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ARG c  73 " --> pdb=" O   SER c  69 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 78 through 83
      removed outlier: 3.599A  pdb=" N   TYR c  83 " --> pdb=" O   LEU c  79 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 137 through 148
      removed outlier: 4.216A  pdb=" N   THR c 141 " --> pdb=" O   ALA c 137 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL c 148 " --> pdb=" O   LYS c 144 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 149 through 160
    Processing helix  chain 'c' and resid 160 through 174
      removed outlier: 3.566A  pdb=" N   LYS c 174 " --> pdb=" O   LEU c 170 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11
      removed outlier: 3.566A  pdb=" N   VAL A  10 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A 112 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19
    Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56
      removed outlier: 3.616A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 5
      removed outlier: 3.751A  pdb=" N   ASN B  75 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER B  63 " --> pdb=" O   ASN B  75 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 55
      removed outlier: 6.795A  pdb=" N   GLU B  46 " --> pdb=" O   ARG B  53 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE B  45 " --> pdb=" O   TRP B  32 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL B  30 " --> pdb=" O   TYR B  47 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU B  88 " --> pdb=" O   TYR B  33 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 126
      removed outlier: 3.667A  pdb=" N   ALA B 124 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU B 144 " --> pdb=" O   ALA B 124 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 157 through 159
      removed outlier: 3.518A  pdb=" N   TRP B 158 " --> pdb=" O   ARG B 207 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG B 207 " --> pdb=" O   TRP B 158 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 41
    Processing sheet with id=AB1, first strand: chain 'C' and resid 7 through 8
      removed outlier: 4.125A  pdb=" N   VAL C  32 " --> pdb=" O   GLY C  24 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 93 through 94
      removed outlier: 3.552A  pdb=" N   ALA C 115 " --> pdb=" O   GLN C  94 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   ASP C 114 " --> pdb=" O   TYR C 121 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 100
      removed outlier: 3.591A  pdb=" N   ASP C 100 " --> pdb=" O   ARG C 109 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 184 through 186
      removed outlier: 3.805A  pdb=" N   LYS C 184 " --> pdb=" O   LEU C 204 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   HIS C 186 " --> pdb=" O   TRP C 202 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   LEU C 204 " --> pdb=" O   LYS C 241 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   LYS C 241 " --> pdb=" O   LEU C 204 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 191 through 192
      removed outlier: 3.704A  pdb=" N   GLU C 196 " --> pdb=" O   ILE C 192 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 211 through 212
    Processing sheet with id=AB7, first strand: chain 'a' and resid 2 through 4
      removed outlier: 4.206A  pdb=" N   SER a   2 " --> pdb=" O   SER a  25 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'a' and resid 10 through 11
      removed outlier: 7.862A  pdb=" N   VAL a  10 " --> pdb=" O   ILE a 112 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'a' and resid 18 through 19
    Processing sheet with id=AC1, first strand: chain 'a' and resid 31 through 35
      removed outlier: 4.268A  pdb=" N   TYR a  31 " --> pdb=" O   ARG a  93 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'a' and resid 55 through 56
    Processing sheet with id=AC3, first strand: chain 'a' and resid 123 through 128
    Processing sheet with id=AC4, first strand: chain 'b' and resid 4 through 5
    Processing sheet with id=AC5, first strand: chain 'b' and resid 32 through 34
      removed outlier: 3.719A  pdb=" N   LEU b  88 " --> pdb=" O   TYR b  33 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'b' and resid 122 through 126
      removed outlier: 3.711A  pdb=" N   ALA b 124 " --> pdb=" O   LEU b 144 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'e' and resid 21 through 22
    Processing sheet with id=AC8, first strand: chain 'e' and resid 39 through 41
    Processing sheet with id=AC9, first strand: chain 'e' and resid 55 through 56
      removed outlier: 3.798A  pdb=" N   SER e  55 " --> pdb=" O   TYR e  63 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR e  63 " --> pdb=" O   SER e  55 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC9
    Processing sheet with id=AD1, first strand: chain 'c' and resid 2 through 3
    Processing sheet with id=AD2, first strand: chain 'c' and resid 33 through 34
      removed outlier: 3.581A  pdb=" N   ALA c  22 " --> pdb=" O   PHE c  34 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   SER c   9 " --> pdb=" O   ILE c  93 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   MET c  96 " --> pdb=" O   GLN c 113 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   ASP c 114 " --> pdb=" O   TYR c 121 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'c' and resid 184 through 188
      removed outlier: 3.648A  pdb=" N   LYS c 184 " --> pdb=" O   LEU c 204 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR c 188 " --> pdb=" O   ARG c 200 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ARG c 200 " --> pdb=" O   THR c 188 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   PHE c 239 " --> pdb=" O   GLY c 205 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN c 240 " --> pdb=" O   ARG c 232 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   ARG c 232 " --> pdb=" O   GLN c 240 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'c' and resid 196 through 197
    Processing sheet with id=AD5, first strand: chain 'c' and resid 211 through 217
      removed outlier: 3.969A  pdb=" N   THR c 212 " --> pdb=" O   GLN c 260 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   GLN c 260 " --> pdb=" O   THR c 212 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   THR c 214 " --> pdb=" O   HIS c 258 " (cutoff:3.500A)

    207 hydrogen bonds defined for protein.
    510 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: 2.36

  Time building geometry restraints manager: 1.39 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: 4251
        1.34 -     1.47: 3329
        1.47 -     1.59: 5489
        1.59 -     1.71: 0
        1.71 -     1.83: 69
  Bond restraints: 13138
  Sorted by residual:
  bond pdb=" C   ARG e   3 "
       pdb=" N   THR e   4 "
    ideal  model  delta    sigma   weight residual
    1.331  1.406 -0.075 2.83e-02 1.25e+03 7.09e+00
  bond pdb=" C   HIS E  31 "
       pdb=" N   PRO E  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.372 -0.038 2.34e-02 1.83e+03 2.62e+00
  bond pdb=" C   HIS e  31 "
       pdb=" N   PRO e  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.369 -0.035 2.34e-02 1.83e+03 2.24e+00
  bond pdb=" N   PRO E   5 "
       pdb=" CA  PRO E   5 "
    ideal  model  delta    sigma   weight residual
    1.469  1.487 -0.018 1.28e-02 6.10e+03 1.96e+00
  bond pdb=" C   GLN B 173 "
       pdb=" O   GLN B 173 "
    ideal  model  delta    sigma   weight residual
    1.249  1.238  0.011 8.50e-03 1.38e+04 1.72e+00
  ... (remaining 13133 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 17499
        2.60 -     5.21: 303
        5.21 -     7.81: 22
        7.81 -    10.41: 8
       10.41 -    13.01: 1
  Bond angle restraints: 17833
  Sorted by residual:
  angle pdb=" N   ALA c  67 "
        pdb=" CA  ALA c  67 "
        pdb=" C   ALA c  67 "
      ideal   model   delta    sigma   weight residual
     113.18  105.18    8.00 1.33e+00 5.65e-01 3.62e+01
  angle pdb=" C   ARG e   3 "
        pdb=" N   THR e   4 "
        pdb=" CA  THR e   4 "
      ideal   model   delta    sigma   weight residual
     120.97  133.98  -13.01 2.84e+00 1.24e-01 2.10e+01
  angle pdb=" C   ASP C 127 "
        pdb=" CA  ASP C 127 "
        pdb=" CB  ASP C 127 "
      ideal   model   delta    sigma   weight residual
     116.63  112.08    4.55 1.16e+00 7.43e-01 1.54e+01
  angle pdb=" C   ARG E   3 "
        pdb=" N   THR E   4 "
        pdb=" CA  THR E   4 "
      ideal   model   delta    sigma   weight residual
     121.80  131.31   -9.51 2.44e+00 1.68e-01 1.52e+01
  angle pdb=" C   PHE e  30 "
        pdb=" N   HIS e  31 "
        pdb=" CA  HIS e  31 "
      ideal   model   delta    sigma   weight residual
     121.80  130.78   -8.98 2.44e+00 1.68e-01 1.35e+01
  ... (remaining 17828 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 6964
       17.45 -    34.90: 687
       34.90 -    52.35: 105
       52.35 -    69.80: 25
       69.80 -    87.25: 23
  Dihedral angle restraints: 7804
    sinusoidal: 3157
      harmonic: 4647
  Sorted by residual:
  dihedral pdb=" CB  CYS C  99 "
           pdb=" SG  CYS C  99 "
           pdb=" SG  CYS C 162 "
           pdb=" CB  CYS C 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    5.75   87.25     1      1.00e+01 1.00e-02 9.14e+01
  dihedral pdb=" CA  HIS E  31 "
           pdb=" C   HIS E  31 "
           pdb=" N   PRO E  32 "
           pdb=" CA  PRO E  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.63  -44.37     0      5.00e+00 4.00e-02 7.88e+01
  dihedral pdb=" CA  HIS e  31 "
           pdb=" C   HIS e  31 "
           pdb=" N   PRO e  32 "
           pdb=" CA  PRO e  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.76  -40.24     0      5.00e+00 4.00e-02 6.48e+01
  ... (remaining 7801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1648
       0.074 -    0.149: 212
       0.149 -    0.223: 5
       0.223 -    0.297: 0
       0.297 -    0.372: 3
  Chirality restraints: 1868
  Sorted by residual:
  chirality pdb=" CB  ILE a 159 "
            pdb=" CA  ILE a 159 "
            pdb=" CG1 ILE a 159 "
            pdb=" CG2 ILE a 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.46e+00
  chirality pdb=" CB  THR a 160 "
            pdb=" CA  THR a 160 "
            pdb=" OG1 THR a 160 "
            pdb=" CG2 THR a 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.20    0.35 2.00e-01 2.50e+01 3.13e+00
  chirality pdb=" CB  ILE A 159 "
            pdb=" CA  ILE A 159 "
            pdb=" CG1 ILE A 159 "
            pdb=" CG2 ILE A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 1865 not shown)

  Planarity restraints: 2350
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  44 "   -0.051 5.00e-02 4.00e+02   7.76e-02 9.62e+00
        pdb=" N   PRO C  45 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO C  45 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C  45 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 169 "   -0.013 2.00e-02 2.50e+03   1.98e-02 7.86e+00
        pdb=" CG  TYR C 169 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 169 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 169 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 169 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 169 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 169 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 169 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP e  60 "   -0.021 2.00e-02 2.50e+03   1.77e-02 7.80e+00
        pdb=" CG  TRP e  60 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP e  60 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP e  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP e  60 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP e  60 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP e  60 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP e  60 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP e  60 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP e  60 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2347 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 707
        2.71 -     3.26: 13518
        3.26 -     3.80: 20544
        3.80 -     4.35: 25158
        4.35 -     4.90: 40547
  Nonbonded interactions: 100474
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E  10 "
            pdb=" O   PRO C 233 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" OH  TYR e  10 "
            pdb=" O   PRO c 233 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" O   ALA a   4 "
            pdb=" OG1 THR a  23 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OD1 ASP E  53 "
            pdb=" NH2 ARG C  46 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OG  SER c  40 "
            pdb=" OE2 GLU c  44 "
     model   vdw
     2.224 3.040
  ... (remaining 100469 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' and (resid 3 through 101 or resid 103 through 104 or (resid 105 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 106 through 115 or  \ 
(resid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 \ 
 or (resid 118 and (name N or name CA or name C or name O or name CB )) or resid \ 
 119 through 148 or resid 154 through 181 or resid 191 through 205))
  selection = (chain 'a' and (resid 3 through 137 or resid 142 through 181 or resid 191 throug \ 
h 205))
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 52 or resid 67 through 132 or resid 134 through  \ 
238))
  selection = chain 'b'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'c' and (resid 1 through 215 or resid 218 through 253 or resid 257 throug \ 
h 265))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'd'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'e'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.170
  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:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.440
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.050
  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:2.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6245
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   0.075  13150  Z= 0.158
  Angle     :  0.793  13.013  17857  Z= 0.425
  Chirality :  0.049   0.372   1868
  Planarity :  0.005   0.078   2350
  Dihedral  : 14.330  84.405   4776
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 22.74
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 17.01 %
    Favored  : 82.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -3.88 (0.20), residues: 1558
  helix: -1.01 (0.42), residues: 137
  sheet: -2.11 (0.24), residues: 405
  loop : -3.21 (0.18), residues: 1016

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B   7 
 TYR   0.048   0.002   TYR C 169 
 PHE   0.036   0.002   PHE b 126 
 TRP   0.048   0.003   TRP e  60 
 HIS   0.008   0.001   HIS a 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (13138)
  covalent geometry    : angle       0.79160 (17833)
  SS BOND              : bond        0.00530 (   12)
  SS BOND              : angle       1.68017 (   24)
  hydrogen bonds       : bond        0.27957 (  207)
  hydrogen bonds       : angle      10.08143 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 355
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7899 (pp30) cc_final: 0.7427 (pp30)
REVERT: A  173 LYS cc_start: 0.8334 (ptpt) cc_final: 0.8072 (ptpt)
REVERT: B   19 LEU cc_start: 0.7121 (mt) cc_final: 0.6420 (mt)
REVERT: B   28 ARG cc_start: 0.6397 (tpt90) cc_final: 0.5724 (tpt-90)
REVERT: B   62 PHE cc_start: 0.7255 (m-80) cc_final: 0.6682 (m-80)
REVERT: B  162 LYS cc_start: 0.8545 (ptpp) cc_final: 0.8201 (ptpp)
REVERT: E   56 PHE cc_start: 0.6023 (p90) cc_final: 0.5536 (p90)
REVERT: E   58 LYS cc_start: 0.7743 (mppt) cc_final: 0.7527 (mmtm)
REVERT: E   81 ARG cc_start: 0.6561 (mtt90) cc_final: 0.5918 (mtt90)
REVERT: E   97 ARG cc_start: 0.7534 (mtt-85) cc_final: 0.6902 (mtt-85)
REVERT: C    3 MET cc_start: 0.6935 (tmm) cc_final: 0.6103 (tmm)
REVERT: C   96 MET cc_start: 0.6761 (tpt) cc_final: 0.6170 (tpt)
REVERT: C  106 ARG cc_start: 0.7083 (ptp-110) cc_final: 0.6729 (ptp-110)
REVERT: C  113 GLN cc_start: 0.7579 (pm20) cc_final: 0.6846 (pm20)
REVERT: C  167 ARG cc_start: 0.8201 (mtm180) cc_final: 0.7815 (mtm110)
REVERT: C  169 TYR cc_start: 0.7342 (m-80) cc_final: 0.6850 (m-80)
REVERT: a   63 GLU cc_start: 0.6671 (pm20) cc_final: 0.6287 (pm20)
REVERT: a  111 LEU cc_start: 0.8425 (tp) cc_final: 0.8165 (tp)
REVERT: b  126 PHE cc_start: 0.7794 (m-80) cc_final: 0.7387 (m-10)
REVERT: b  144 LEU cc_start: 0.8247 (mp) cc_final: 0.7700 (mp)
REVERT: b  191 ARG cc_start: 0.6982 (pmt-80) cc_final: 0.6767 (pmt-80)
REVERT: b  231 GLN cc_start: 0.6976 (mt0) cc_final: 0.6467 (mp10)
REVERT: e   58 LYS cc_start: 0.7804 (tmtt) cc_final: 0.7464 (tmtt)
REVERT: c    4 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6940 (mtp-110)
REVERT: c   12 ARG cc_start: 0.7846 (pmt170) cc_final: 0.7448 (pmt170)
REVERT: c   27 ASP cc_start: 0.7596 (t70) cc_final: 0.7329 (t70)
REVERT: c   41 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7616 (tp-100)
REVERT: c  113 GLN cc_start: 0.7974 (pt0) cc_final: 0.7708 (pt0)
REVERT: c  122 ILE cc_start: 0.8031 (tt) cc_final: 0.7823 (tt)
REVERT: c  153 GLN cc_start: 0.7016 (tp40) cc_final: 0.6543 (tp40)
REVERT: c  167 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7926 (mtm-85)
REVERT: c  171 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6600 (tm-30)
REVERT: c  230 GLU cc_start: 0.5801 (tm-30) cc_final: 0.5356 (tm-30)
REVERT: c  252 GLU cc_start: 0.8296 (mp0) cc_final: 0.7975 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 355
  average time/residue: 0.1360
  time to fit residues: 67.2757
Evaluate side-chains
  341 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 341
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    3.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
e   2 GLN
** c 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** c 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.176531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.149307 restraints weight = 22473.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.154915 restraints weight = 13312.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.158856 restraints weight = 8805.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.161715 restraints weight = 6252.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.163496 restraints weight = 4696.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6329
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  13150  Z= 0.300
  Angle     :  0.840  11.513  17857  Z= 0.447
  Chirality :  0.050   0.305   1868
  Planarity :  0.006   0.059   2350
  Dihedral  :  6.673  44.030   1753
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 22.87
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 20.60 %
    Favored  : 79.01 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  5.51 %
    Favored  : 94.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -4.00 (0.20), residues: 1558
  helix: -0.84 (0.42), residues: 139
  sheet: -2.25 (0.24), residues: 439
  loop : -3.32 (0.18), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG c 167 
 TYR   0.027   0.002   TYR E  10 
 PHE   0.035   0.003   PHE E  30 
 TRP   0.035   0.003   TRP e  60 
 HIS   0.012   0.002   HIS c  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00609 (13138)
  covalent geometry    : angle       0.83598 (17833)
  SS BOND              : bond        0.00824 (   12)
  SS BOND              : angle       2.30226 (   24)
  hydrogen bonds       : bond        0.07156 (  207)
  hydrogen bonds       : angle       8.39308 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 367
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7768 (pp30) cc_final: 0.7111 (pp30)
REVERT: A   48 LYS cc_start: 0.7512 (mmmt) cc_final: 0.7282 (mmmt)
REVERT: A   63 GLU cc_start: 0.6888 (pm20) cc_final: 0.6549 (pm20)
REVERT: B   15 GLN cc_start: 0.7774 (mp10) cc_final: 0.7553 (mp10)
REVERT: B   62 PHE cc_start: 0.7331 (m-80) cc_final: 0.6740 (m-80)
REVERT: B   87 TYR cc_start: 0.7160 (m-80) cc_final: 0.6847 (m-80)
REVERT: B  162 LYS cc_start: 0.8666 (ptpp) cc_final: 0.8342 (ptpp)
REVERT: B  192 LEU cc_start: 0.8077 (mm) cc_final: 0.7809 (mm)
REVERT: E    6 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7981 (ttmt)
REVERT: E   12 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8033 (mtt180)
REVERT: E   56 PHE cc_start: 0.6205 (p90) cc_final: 0.5823 (p90)
REVERT: E   58 LYS cc_start: 0.7824 (mppt) cc_final: 0.7571 (mmtm)
REVERT: C    3 MET cc_start: 0.7162 (tmm) cc_final: 0.6791 (tmm)
REVERT: C  106 ARG cc_start: 0.7165 (ptp-110) cc_final: 0.6831 (ptp-110)
REVERT: C  122 ILE cc_start: 0.8312 (tt) cc_final: 0.8076 (tt)
REVERT: C  223 THR cc_start: 0.8008 (p) cc_final: 0.7803 (p)
REVERT: a   21 LYS cc_start: 0.7439 (ttmm) cc_final: 0.6910 (ttmm)
REVERT: a   63 GLU cc_start: 0.7084 (pm20) cc_final: 0.6609 (pm20)
REVERT: a  165 LEU cc_start: 0.6760 (pp) cc_final: 0.6317 (pp)
REVERT: b  191 ARG cc_start: 0.7031 (pmt-80) cc_final: 0.6417 (pmt-80)
REVERT: e   58 LYS cc_start: 0.7914 (tmtt) cc_final: 0.7695 (tmtt)
REVERT: e   96 ASP cc_start: 0.7754 (p0) cc_final: 0.6282 (p0)
REVERT: c    4 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7106 (mtp-110)
REVERT: c    7 PHE cc_start: 0.6476 (m-10) cc_final: 0.5807 (m-10)
REVERT: c   12 ARG cc_start: 0.7841 (pmt170) cc_final: 0.7382 (pmt170)
REVERT: c   20 PHE cc_start: 0.8114 (t80) cc_final: 0.7501 (t80)
REVERT: c   27 ASP cc_start: 0.7656 (t70) cc_final: 0.7044 (t70)
REVERT: c   46 ARG cc_start: 0.7096 (ptp-170) cc_final: 0.6896 (ptp-170)
REVERT: c   60 GLN cc_start: 0.8639 (tt0) cc_final: 0.8409 (tt0)
REVERT: c   96 MET cc_start: 0.6270 (tmm) cc_final: 0.5610 (tmm)
REVERT: c   97 TYR cc_start: 0.6198 (m-10) cc_final: 0.5427 (m-10)
REVERT: c  113 GLN cc_start: 0.7900 (pt0) cc_final: 0.7605 (pt0)
REVERT: c  122 ILE cc_start: 0.8326 (tt) cc_final: 0.8046 (tt)
REVERT: c  171 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6686 (tm-30)
REVERT: c  195 HIS cc_start: 0.6811 (m-70) cc_final: 0.6376 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 368
  average time/residue: 0.1310
  time to fit residues: 67.5951
Evaluate side-chains
  355 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 354
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 147 optimal weight:    5.9990
   chunk 129 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 98 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 117 optimal weight:    6.9990
   chunk 149 optimal weight:    6.9990
   chunk 76 optimal weight:    0.5980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  35 GLN
c  94 GLN
** c 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.177134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.149534 restraints weight = 22538.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.155203 restraints weight = 13339.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.159179 restraints weight = 8809.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.161968 restraints weight = 6290.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.163786 restraints weight = 4761.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6311
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13150  Z= 0.248
  Angle     :  0.803  11.555  17857  Z= 0.425
  Chirality :  0.050   0.321   1868
  Planarity :  0.006   0.063   2350
  Dihedral  :  6.696  44.847   1753
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 21.02
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 20.09 %
    Favored  : 79.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -3.98 (0.20), residues: 1558
  helix: -0.73 (0.42), residues: 138
  sheet: -2.28 (0.24), residues: 437
  loop : -3.29 (0.18), residues: 983

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG c 167 
 TYR   0.025   0.002   TYR E  10 
 PHE   0.038   0.003   PHE B 126 
 TRP   0.026   0.003   TRP e  60 
 HIS   0.007   0.002   HIS C   1 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 (13138)
  covalent geometry    : angle       0.80106 (17833)
  SS BOND              : bond        0.01021 (   12)
  SS BOND              : angle       1.85336 (   24)
  hydrogen bonds       : bond        0.05555 (  207)
  hydrogen bonds       : angle       8.01590 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 368
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7755 (pp30) cc_final: 0.7173 (pp30)
REVERT: A  131 LYS cc_start: 0.8969 (ptpt) cc_final: 0.8740 (ptpt)
REVERT: B   62 PHE cc_start: 0.7312 (m-80) cc_final: 0.6802 (m-80)
REVERT: B  158 TRP cc_start: 0.6639 (m100) cc_final: 0.6227 (m100)
REVERT: B  162 LYS cc_start: 0.8720 (ptpp) cc_final: 0.8226 (ptpp)
REVERT: B  192 LEU cc_start: 0.8074 (mm) cc_final: 0.7779 (mm)
REVERT: E   12 ARG cc_start: 0.8540 (mtt180) cc_final: 0.7994 (mtt180)
REVERT: E   58 LYS cc_start: 0.7844 (mppt) cc_final: 0.7627 (mmtm)
REVERT: E   81 ARG cc_start: 0.6612 (mtt90) cc_final: 0.5948 (mtt90)
REVERT: E   96 ASP cc_start: 0.8096 (p0) cc_final: 0.7793 (p0)
REVERT: C  106 ARG cc_start: 0.7148 (ptp-110) cc_final: 0.6789 (ptp-110)
REVERT: C  122 ILE cc_start: 0.8346 (tt) cc_final: 0.8110 (tt)
REVERT: C  136 MET cc_start: 0.3597 (mtt) cc_final: 0.3076 (mtt)
REVERT: C  171 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6297 (tm-30)
REVERT: a   63 GLU cc_start: 0.7144 (pm20) cc_final: 0.6771 (pm20)
REVERT: a   84 ASP cc_start: 0.8279 (m-30) cc_final: 0.8045 (m-30)
REVERT: b  127 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7337 (mt-10)
REVERT: b  144 LEU cc_start: 0.8089 (mp) cc_final: 0.7877 (mp)
REVERT: b  148 PHE cc_start: 0.7362 (p90) cc_final: 0.7117 (p90)
REVERT: b  191 ARG cc_start: 0.7000 (pmt-80) cc_final: 0.6484 (pmt-80)
REVERT: c    7 PHE cc_start: 0.6438 (m-10) cc_final: 0.5817 (m-10)
REVERT: c   20 PHE cc_start: 0.8120 (t80) cc_final: 0.7506 (t80)
REVERT: c   27 ASP cc_start: 0.7624 (t70) cc_final: 0.7053 (t70)
REVERT: c   46 ARG cc_start: 0.7080 (ptp-170) cc_final: 0.6868 (ptp-170)
REVERT: c   96 MET cc_start: 0.6713 (tmm) cc_final: 0.5703 (tmm)
REVERT: c   97 TYR cc_start: 0.6193 (m-10) cc_final: 0.5440 (m-10)
REVERT: c  113 GLN cc_start: 0.8063 (pt0) cc_final: 0.7707 (pt0)
REVERT: c  122 ILE cc_start: 0.8356 (tt) cc_final: 0.8085 (tt)
REVERT: c  195 HIS cc_start: 0.6588 (m-70) cc_final: 0.6215 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 368
  average time/residue: 0.1285
  time to fit residues: 66.2771
Evaluate side-chains
  352 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 352
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0010
   chunk 80 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 136 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 105 optimal weight:    0.0370
   chunk 91 optimal weight:   10.0000
   overall best weight:    0.3864

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

Flipped N/Q/H residues before XYZ refinement:
** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   2 GLN
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C   1 HIS
C 195 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.182784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.155020 restraints weight = 22410.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.160726 restraints weight = 13228.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.164690 restraints weight = 8725.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.167586 restraints weight = 6238.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.169442 restraints weight = 4747.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6160
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13150  Z= 0.132
  Angle     :  0.724  11.475  17857  Z= 0.375
  Chirality :  0.047   0.334   1868
  Planarity :  0.005   0.063   2350
  Dihedral  :  6.111  43.246   1753
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 15.47 %
    Favored  : 84.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -3.72 (0.20), residues: 1558
  helix: -0.52 (0.42), residues: 136
  sheet: -2.10 (0.24), residues: 443
  loop : -3.11 (0.19), residues: 979

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  45 
 TYR   0.021   0.001   TYR A  60 
 PHE   0.025   0.002   PHE b 126 
 TRP   0.020   0.002   TRP B  32 
 HIS   0.005   0.001   HIS c 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13138)
  covalent geometry    : angle       0.72283 (17833)
  SS BOND              : bond        0.00477 (   12)
  SS BOND              : angle       1.48395 (   24)
  hydrogen bonds       : bond        0.04269 (  207)
  hydrogen bonds       : angle       7.25797 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 355
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7782 (pp30) cc_final: 0.7176 (pp30)
REVERT: A   63 GLU cc_start: 0.6905 (pm20) cc_final: 0.6559 (pm20)
REVERT: A  173 LYS cc_start: 0.8326 (ptpt) cc_final: 0.8074 (ptpt)
REVERT: B   62 PHE cc_start: 0.7405 (m-80) cc_final: 0.6882 (m-80)
REVERT: B   87 TYR cc_start: 0.6846 (m-80) cc_final: 0.5997 (m-80)
REVERT: B  141 LEU cc_start: 0.8345 (mp) cc_final: 0.8135 (mp)
REVERT: B  192 LEU cc_start: 0.8074 (mm) cc_final: 0.7667 (mm)
REVERT: E    2 GLN cc_start: 0.6931 (mm-40) cc_final: 0.6687 (mm-40)
REVERT: E   12 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7633 (mtt180)
REVERT: E   58 LYS cc_start: 0.7854 (mppt) cc_final: 0.7594 (mmtm)
REVERT: E   96 ASP cc_start: 0.8073 (p0) cc_final: 0.7702 (p0)
REVERT: C   19 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7810 (ttm110)
REVERT: C  136 MET cc_start: 0.3101 (mtt) cc_final: 0.2563 (mtt)
REVERT: C  167 ARG cc_start: 0.8250 (mtm180) cc_final: 0.7832 (mtm110)
REVERT: C  171 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6205 (tm-30)
REVERT: a   41 ARG cc_start: 0.6734 (ttt-90) cc_final: 0.6169 (ttt180)
REVERT: a   63 GLU cc_start: 0.6965 (pm20) cc_final: 0.6628 (pm20)
REVERT: a   74 HIS cc_start: 0.6932 (m90) cc_final: 0.6698 (m90)
REVERT: a   84 ASP cc_start: 0.8063 (m-30) cc_final: 0.7821 (m-30)
REVERT: a  165 LEU cc_start: 0.6822 (pp) cc_final: 0.6470 (pp)
REVERT: b  144 LEU cc_start: 0.8186 (mp) cc_final: 0.7935 (mp)
REVERT: b  191 ARG cc_start: 0.6983 (pmt-80) cc_final: 0.6417 (pmt-80)
REVERT: e   58 LYS cc_start: 0.7882 (tmtt) cc_final: 0.7635 (tmtt)
REVERT: c    7 PHE cc_start: 0.6473 (m-10) cc_final: 0.5790 (m-10)
REVERT: c   27 ASP cc_start: 0.7538 (t70) cc_final: 0.7179 (t70)
REVERT: c   46 ARG cc_start: 0.7057 (ptp-170) cc_final: 0.6734 (ptt-90)
REVERT: c   96 MET cc_start: 0.6175 (tmm) cc_final: 0.5538 (tmm)
REVERT: c   97 TYR cc_start: 0.5761 (m-10) cc_final: 0.4912 (m-10)
REVERT: c  122 ILE cc_start: 0.8108 (tt) cc_final: 0.7795 (tt)
REVERT: c  171 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6649 (tm-30)
REVERT: c  195 HIS cc_start: 0.6536 (m-70) cc_final: 0.6145 (m-70)
REVERT: d    6 TYR cc_start: 0.6527 (m-80) cc_final: 0.6311 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 355
  average time/residue: 0.1344
  time to fit residues: 66.7047
Evaluate side-chains
  338 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 338
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 109 optimal weight:    7.9990
   chunk 133 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 117 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c  94 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.181127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.153352 restraints weight = 22407.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.159221 restraints weight = 12990.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.163298 restraints weight = 8463.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.166185 restraints weight = 5964.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.168062 restraints weight = 4474.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6277
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  13150  Z= 0.222
  Angle     :  0.782  11.578  17857  Z= 0.409
  Chirality :  0.049   0.284   1868
  Planarity :  0.005   0.059   2350
  Dihedral  :  6.470  43.260   1753
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 19.90 %
    Favored  : 79.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    Twisted General : 0.07 %

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: -3.82 (0.20), residues: 1558
  helix: -0.47 (0.43), residues: 139
  sheet: -2.14 (0.24), residues: 440
  loop : -3.23 (0.19), residues: 979

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG c 167 
 TYR   0.022   0.002   TYR c 157 
 PHE   0.036   0.002   PHE B 102 
 TRP   0.026   0.002   TRP e  60 
 HIS   0.007   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (13138)
  covalent geometry    : angle       0.77972 (17833)
  SS BOND              : bond        0.00839 (   12)
  SS BOND              : angle       1.80624 (   24)
  hydrogen bonds       : bond        0.04795 (  207)
  hydrogen bonds       : angle       7.39826 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 355
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7845 (pp30) cc_final: 0.7419 (pp30)
REVERT: A   48 LYS cc_start: 0.7384 (mmtm) cc_final: 0.7124 (mmtm)
REVERT: A  170 MET cc_start: 0.7138 (tmm) cc_final: 0.6795 (tmm)
REVERT: A  173 LYS cc_start: 0.8368 (ptpt) cc_final: 0.8084 (ptpt)
REVERT: B   62 PHE cc_start: 0.7408 (m-80) cc_final: 0.6833 (m-80)
REVERT: B   87 TYR cc_start: 0.6996 (m-80) cc_final: 0.6346 (m-80)
REVERT: B  192 LEU cc_start: 0.8041 (mm) cc_final: 0.7773 (mm)
REVERT: E   12 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7868 (mtt180)
REVERT: E   45 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.8053 (mtp-110)
REVERT: E   58 LYS cc_start: 0.7833 (mppt) cc_final: 0.7607 (mmtm)
REVERT: E   81 ARG cc_start: 0.6564 (mtt90) cc_final: 0.5871 (mtt90)
REVERT: E   96 ASP cc_start: 0.8053 (p0) cc_final: 0.7847 (p0)
REVERT: C  106 ARG cc_start: 0.7213 (ptp-110) cc_final: 0.6883 (ptp-110)
REVERT: C  187 MET cc_start: 0.3730 (ppp) cc_final: 0.3508 (ppp)
REVERT: a   41 ARG cc_start: 0.6901 (ttt-90) cc_final: 0.6425 (ttt180)
REVERT: a   63 GLU cc_start: 0.7112 (pm20) cc_final: 0.6674 (pm20)
REVERT: a  165 LEU cc_start: 0.6750 (pp) cc_final: 0.6407 (pp)
REVERT: b  127 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7090 (mt-10)
REVERT: b  144 LEU cc_start: 0.8165 (mp) cc_final: 0.7964 (mp)
REVERT: b  155 LEU cc_start: 0.8590 (mt) cc_final: 0.8339 (mt)
REVERT: b  169 CYS cc_start: 0.7532 (p) cc_final: 0.7084 (p)
REVERT: b  191 ARG cc_start: 0.6903 (pmt-80) cc_final: 0.6293 (pmt-80)
REVERT: e   30 PHE cc_start: 0.6150 (m-10) cc_final: 0.5792 (m-10)
REVERT: c    7 PHE cc_start: 0.6485 (m-10) cc_final: 0.5821 (m-10)
REVERT: c   20 PHE cc_start: 0.8064 (t80) cc_final: 0.7424 (t80)
REVERT: c   63 ARG cc_start: 0.7783 (tmt-80) cc_final: 0.7393 (tmt-80)
REVERT: c   72 ASP cc_start: 0.7631 (m-30) cc_final: 0.7212 (m-30)
REVERT: c   76 LEU cc_start: 0.7873 (mp) cc_final: 0.7608 (mp)
REVERT: c   96 MET cc_start: 0.6157 (tmm) cc_final: 0.5641 (tmm)
REVERT: c   97 TYR cc_start: 0.5999 (m-10) cc_final: 0.5285 (m-10)
REVERT: c  113 GLN cc_start: 0.7854 (pt0) cc_final: 0.7503 (pt0)
REVERT: c  122 ILE cc_start: 0.8320 (tt) cc_final: 0.8013 (tt)
REVERT: c  184 LYS cc_start: 0.7348 (ptpp) cc_final: 0.6819 (ptpp)
REVERT: c  195 HIS cc_start: 0.6721 (m-70) cc_final: 0.6298 (m-70)
REVERT: d    6 TYR cc_start: 0.6555 (m-80) cc_final: 0.6349 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 355
  average time/residue: 0.1314
  time to fit residues: 65.1190
Evaluate side-chains
  341 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 341
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 135 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0270
   chunk 92 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 78 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 125 optimal weight:    0.0980
   overall best weight:    1.2244

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

Flipped N/Q/H residues before XYZ refinement:
** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.178698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.151608 restraints weight = 22466.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.157065 restraints weight = 13359.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.160928 restraints weight = 8855.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.163665 restraints weight = 6350.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.165731 restraints weight = 4851.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6216
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13150  Z= 0.166
  Angle     :  0.755  11.357  17857  Z= 0.392
  Chirality :  0.049   0.377   1868
  Planarity :  0.005   0.072   2350
  Dihedral  :  6.282  42.850   1753
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 17.20 %
    Favored  : 82.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -3.79 (0.20), residues: 1558
  helix: -0.58 (0.42), residues: 136
  sheet: -2.22 (0.24), residues: 443
  loop : -3.12 (0.19), residues: 979

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG c 167 
 TYR   0.019   0.002   TYR E  10 
 PHE   0.041   0.002   PHE B 126 
 TRP   0.021   0.002   TRP e  60 
 HIS   0.007   0.001   HIS A 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (13138)
  covalent geometry    : angle       0.75206 (17833)
  SS BOND              : bond        0.00913 (   12)
  SS BOND              : angle       2.09569 (   24)
  hydrogen bonds       : bond        0.04339 (  207)
  hydrogen bonds       : angle       7.16368 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 352
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7846 (pp30) cc_final: 0.7398 (pp30)
REVERT: A   68 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8520 (mmmt)
REVERT: A  170 MET cc_start: 0.7082 (tmm) cc_final: 0.6800 (tmm)
REVERT: A  173 LYS cc_start: 0.8353 (ptpt) cc_final: 0.8099 (ptpt)
REVERT: B   62 PHE cc_start: 0.7341 (m-80) cc_final: 0.6844 (m-80)
REVERT: B   87 TYR cc_start: 0.6799 (m-80) cc_final: 0.6098 (m-80)
REVERT: B  126 PHE cc_start: 0.7123 (m-80) cc_final: 0.6888 (m-80)
REVERT: B  192 LEU cc_start: 0.8050 (mm) cc_final: 0.7785 (mm)
REVERT: E   12 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7711 (mtt180)
REVERT: E   58 LYS cc_start: 0.7783 (mppt) cc_final: 0.7568 (mmtm)
REVERT: E   96 ASP cc_start: 0.8093 (p0) cc_final: 0.7877 (p0)
REVERT: C   96 MET cc_start: 0.6567 (tpt) cc_final: 0.6290 (tpt)
REVERT: C  107 PHE cc_start: 0.8159 (t80) cc_final: 0.7933 (t80)
REVERT: a   21 LYS cc_start: 0.7498 (ttmm) cc_final: 0.7192 (ttmm)
REVERT: a   41 ARG cc_start: 0.6836 (ttt-90) cc_final: 0.6296 (ttt180)
REVERT: a   63 GLU cc_start: 0.7007 (pm20) cc_final: 0.6674 (pm20)
REVERT: a   74 HIS cc_start: 0.6969 (m90) cc_final: 0.6479 (m90)
REVERT: b  144 LEU cc_start: 0.8159 (mp) cc_final: 0.7930 (mp)
REVERT: b  191 ARG cc_start: 0.6916 (pmt-80) cc_final: 0.6503 (pmt-80)
REVERT: e   58 LYS cc_start: 0.7885 (tmtt) cc_final: 0.7679 (tmtt)
REVERT: c    7 PHE cc_start: 0.6541 (m-10) cc_final: 0.6001 (m-10)
REVERT: c   63 ARG cc_start: 0.7737 (tmt-80) cc_final: 0.7494 (tmt-80)
REVERT: c   76 LEU cc_start: 0.7653 (mp) cc_final: 0.7364 (mp)
REVERT: c   96 MET cc_start: 0.6283 (tmm) cc_final: 0.5922 (tmm)
REVERT: c   97 TYR cc_start: 0.5899 (m-10) cc_final: 0.5228 (m-10)
REVERT: c  122 ILE cc_start: 0.8205 (tt) cc_final: 0.7920 (tt)
REVERT: c  184 LYS cc_start: 0.7374 (ptpp) cc_final: 0.6857 (ptpp)
REVERT: c  195 HIS cc_start: 0.6584 (m-70) cc_final: 0.6176 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 352
  average time/residue: 0.1336
  time to fit residues: 65.8570
Evaluate side-chains
  339 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 339
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 86 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 93 optimal weight:    5.9990
   chunk 149 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    7.9990
   chunk 120 optimal weight:    0.7980
   chunk 124 optimal weight:   10.0000
   chunk 122 optimal weight:    0.0030
   chunk 146 optimal weight:    5.9990
   overall best weight:    1.3394

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

Flipped N/Q/H residues before XYZ refinement:
** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C   1 HIS
C 190 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.180987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.153849 restraints weight = 22260.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.159530 restraints weight = 13042.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.163485 restraints weight = 8532.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.166330 restraints weight = 6048.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.168128 restraints weight = 4541.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6217
moved from start:          0.2388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13150  Z= 0.172
  Angle     :  0.754  11.416  17857  Z= 0.391
  Chirality :  0.049   0.346   1868
  Planarity :  0.005   0.081   2350
  Dihedral  :  6.267  42.959   1753
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 18.42 %
    Favored  : 81.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -3.85 (0.20), residues: 1558
  helix: -0.58 (0.42), residues: 140
  sheet: -2.25 (0.23), residues: 459
  loop : -3.18 (0.19), residues: 959

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG c 167 
 TYR   0.021   0.002   TYR B 213 
 PHE   0.035   0.002   PHE B 126 
 TRP   0.027   0.002   TRP b  32 
 HIS   0.007   0.001   HIS a 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13138)
  covalent geometry    : angle       0.75229 (17833)
  SS BOND              : bond        0.00700 (   12)
  SS BOND              : angle       1.69437 (   24)
  hydrogen bonds       : bond        0.04355 (  207)
  hydrogen bonds       : angle       7.07775 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 350
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7791 (pp30) cc_final: 0.7382 (pp30)
REVERT: A   68 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8506 (mmmt)
REVERT: A  173 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8123 (ptpt)
REVERT: B   62 PHE cc_start: 0.7355 (m-80) cc_final: 0.6948 (m-80)
REVERT: B   87 TYR cc_start: 0.6810 (m-80) cc_final: 0.6071 (m-80)
REVERT: B  192 LEU cc_start: 0.8071 (mm) cc_final: 0.7677 (mm)
REVERT: E   12 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7720 (mtt180)
REVERT: E   60 TRP cc_start: 0.6796 (m100) cc_final: 0.6581 (m100)
REVERT: C   12 ARG cc_start: 0.7538 (mpp80) cc_final: 0.7234 (mtm-85)
REVERT: C   96 MET cc_start: 0.6519 (tpt) cc_final: 0.6162 (tpt)
REVERT: C  107 PHE cc_start: 0.8184 (t80) cc_final: 0.7954 (t80)
REVERT: a   41 ARG cc_start: 0.6900 (ttt-90) cc_final: 0.6355 (ttt180)
REVERT: a   63 GLU cc_start: 0.7057 (pm20) cc_final: 0.6707 (pm20)
REVERT: a   84 ASP cc_start: 0.8245 (m-30) cc_final: 0.7996 (m-30)
REVERT: a  111 LEU cc_start: 0.8489 (tp) cc_final: 0.8274 (tp)
REVERT: b  127 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7049 (mt-10)
REVERT: b  144 LEU cc_start: 0.8185 (mp) cc_final: 0.7970 (mp)
REVERT: e   58 LYS cc_start: 0.7877 (tmtt) cc_final: 0.7674 (tmtt)
REVERT: c    7 PHE cc_start: 0.6518 (m-10) cc_final: 0.5973 (m-10)
REVERT: c   19 ARG cc_start: 0.7389 (ttm110) cc_final: 0.7138 (ttm110)
REVERT: c   46 ARG cc_start: 0.7076 (ptp-170) cc_final: 0.6793 (ptp-170)
REVERT: c   63 ARG cc_start: 0.7635 (tmt-80) cc_final: 0.7391 (tmt-80)
REVERT: c   76 LEU cc_start: 0.7621 (mp) cc_final: 0.7347 (mp)
REVERT: c   96 MET cc_start: 0.6300 (tmm) cc_final: 0.5986 (tmm)
REVERT: c   97 TYR cc_start: 0.5943 (m-10) cc_final: 0.5273 (m-10)
REVERT: c  122 ILE cc_start: 0.8268 (tt) cc_final: 0.7964 (tt)
REVERT: c  167 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7903 (mtm-85)
REVERT: c  184 LYS cc_start: 0.7379 (ptpp) cc_final: 0.6843 (ptpp)
REVERT: c  195 HIS cc_start: 0.6634 (m-70) cc_final: 0.6220 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 350
  average time/residue: 0.1277
  time to fit residues: 62.6220
Evaluate side-chains
  338 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 338
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 149 optimal weight:    6.9990
   chunk 53 optimal weight:    0.7980
   chunk 147 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 108 optimal weight:    6.9990
   chunk 121 optimal weight:    3.9990
   chunk 113 optimal weight:   10.0000
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.178816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.153038 restraints weight = 22475.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.158354 restraints weight = 13440.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.162065 restraints weight = 8899.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.164733 restraints weight = 6367.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.166491 restraints weight = 4812.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6222
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13150  Z= 0.180
  Angle     :  0.770  11.278  17857  Z= 0.399
  Chirality :  0.049   0.334   1868
  Planarity :  0.005   0.074   2350
  Dihedral  :  6.298  42.864   1753
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 18.36 %
    Favored  : 81.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -3.83 (0.20), residues: 1558
  helix: -0.53 (0.42), residues: 140
  sheet: -2.26 (0.24), residues: 449
  loop : -3.16 (0.19), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  15 
 TYR   0.019   0.002   TYR E  10 
 PHE   0.032   0.002   PHE E  30 
 TRP   0.037   0.002   TRP E  95 
 HIS   0.005   0.001   HIS c  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (13138)
  covalent geometry    : angle       0.76607 (17833)
  SS BOND              : bond        0.00814 (   12)
  SS BOND              : angle       2.12731 (   24)
  hydrogen bonds       : bond        0.04286 (  207)
  hydrogen bonds       : angle       7.03922 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 348
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7802 (pp30) cc_final: 0.7369 (pp30)
REVERT: A   68 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8517 (mmmt)
REVERT: A  173 LYS cc_start: 0.8404 (ptpt) cc_final: 0.8139 (ptpt)
REVERT: B   11 LYS cc_start: 0.7467 (ttmm) cc_final: 0.7204 (ttmm)
REVERT: B   62 PHE cc_start: 0.7340 (m-80) cc_final: 0.6947 (m-80)
REVERT: B   87 TYR cc_start: 0.6857 (m-80) cc_final: 0.6119 (m-80)
REVERT: B  192 LEU cc_start: 0.8081 (mm) cc_final: 0.7762 (mm)
REVERT: E   12 ARG cc_start: 0.8420 (mtt180) cc_final: 0.7722 (mtt180)
REVERT: E   58 LYS cc_start: 0.7836 (mppt) cc_final: 0.7547 (mmtm)
REVERT: C   19 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8054 (ttm110)
REVERT: C  107 PHE cc_start: 0.8177 (t80) cc_final: 0.7944 (t80)
REVERT: a   21 LYS cc_start: 0.7485 (ttmm) cc_final: 0.7169 (ttmm)
REVERT: a   41 ARG cc_start: 0.6911 (ttt-90) cc_final: 0.6405 (ttt-90)
REVERT: a   63 GLU cc_start: 0.7058 (pm20) cc_final: 0.6741 (pm20)
REVERT: a   74 HIS cc_start: 0.6994 (m90) cc_final: 0.6507 (m90)
REVERT: a  111 LEU cc_start: 0.8463 (tp) cc_final: 0.8247 (tp)
REVERT: b  127 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7062 (mt-10)
REVERT: b  144 LEU cc_start: 0.8217 (mp) cc_final: 0.7989 (mp)
REVERT: e   58 LYS cc_start: 0.7905 (tmtt) cc_final: 0.7689 (tmtt)
REVERT: e   99 MET cc_start: 0.4267 (mtt) cc_final: 0.4065 (mtt)
REVERT: c    7 PHE cc_start: 0.6548 (m-10) cc_final: 0.5984 (m-10)
REVERT: c   19 ARG cc_start: 0.7381 (ttm110) cc_final: 0.7180 (ttm110)
REVERT: c   46 ARG cc_start: 0.7067 (ptp-170) cc_final: 0.6688 (ptp90)
REVERT: c   76 LEU cc_start: 0.7632 (mp) cc_final: 0.7348 (mp)
REVERT: c   96 MET cc_start: 0.6276 (tmm) cc_final: 0.5994 (tmm)
REVERT: c   97 TYR cc_start: 0.5963 (m-10) cc_final: 0.5315 (m-10)
REVERT: c  122 ILE cc_start: 0.8261 (tt) cc_final: 0.7952 (tt)
REVERT: c  184 LYS cc_start: 0.7402 (ptpp) cc_final: 0.6848 (ptpp)
REVERT: c  195 HIS cc_start: 0.6655 (m-70) cc_final: 0.6243 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 348
  average time/residue: 0.1287
  time to fit residues: 62.7325
Evaluate side-chains
  338 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 338
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 147 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 88 optimal weight:    8.9990
   chunk 128 optimal weight:    4.9990
   chunk 93 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   chunk 151 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 142 optimal weight:    1.9990
   chunk 137 optimal weight:    0.7980
   chunk 74 optimal weight:    0.5980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.181183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.153834 restraints weight = 22313.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.159551 restraints weight = 13067.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.163540 restraints weight = 8561.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.166364 restraints weight = 6062.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.168431 restraints weight = 4564.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6205
moved from start:          0.2587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13150  Z= 0.169
  Angle     :  0.767  11.298  17857  Z= 0.397
  Chirality :  0.050   0.337   1868
  Planarity :  0.005   0.072   2350
  Dihedral  :  6.284  42.711   1753
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 18.36 %
    Favored  : 81.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -3.80 (0.20), residues: 1558
  helix: -0.51 (0.43), residues: 140
  sheet: -2.23 (0.23), residues: 451
  loop : -3.14 (0.19), residues: 967

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG c 167 
 TYR   0.025   0.002   TYR B  47 
 PHE   0.030   0.002   PHE A  73 
 TRP   0.033   0.002   TRP E  95 
 HIS   0.005   0.001   HIS c 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13138)
  covalent geometry    : angle       0.76498 (17833)
  SS BOND              : bond        0.00688 (   12)
  SS BOND              : angle       1.72981 (   24)
  hydrogen bonds       : bond        0.04194 (  207)
  hydrogen bonds       : angle       6.91370 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 350
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7922 (pp30) cc_final: 0.7585 (pp30)
REVERT: A   63 GLU cc_start: 0.6914 (pm20) cc_final: 0.6488 (pm20)
REVERT: A   68 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8505 (mmmt)
REVERT: A  173 LYS cc_start: 0.8416 (ptpt) cc_final: 0.8136 (ptpt)
REVERT: B   62 PHE cc_start: 0.7326 (m-80) cc_final: 0.6929 (m-80)
REVERT: B   87 TYR cc_start: 0.6755 (m-80) cc_final: 0.5979 (m-80)
REVERT: B  192 LEU cc_start: 0.8084 (mm) cc_final: 0.7764 (mm)
REVERT: E   12 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7703 (mtt180)
REVERT: C    7 PHE cc_start: 0.6644 (m-10) cc_final: 0.6407 (m-10)
REVERT: C   19 ARG cc_start: 0.8242 (ttm110) cc_final: 0.8005 (ttm110)
REVERT: C  107 PHE cc_start: 0.8175 (t80) cc_final: 0.7954 (t80)
REVERT: a   41 ARG cc_start: 0.6936 (ttt-90) cc_final: 0.6428 (ttt-90)
REVERT: a   63 GLU cc_start: 0.7067 (pm20) cc_final: 0.6751 (pm20)
REVERT: a  111 LEU cc_start: 0.8459 (tp) cc_final: 0.8232 (tp)
REVERT: b   19 LEU cc_start: 0.6485 (mt) cc_final: 0.5973 (mt)
REVERT: b  144 LEU cc_start: 0.8185 (mp) cc_final: 0.7974 (mp)
REVERT: e   58 LYS cc_start: 0.7911 (tmtt) cc_final: 0.7674 (tmtt)
REVERT: e   99 MET cc_start: 0.4272 (mtt) cc_final: 0.4065 (mtt)
REVERT: c    7 PHE cc_start: 0.6555 (m-10) cc_final: 0.5979 (m-10)
REVERT: c   19 ARG cc_start: 0.7366 (ttm110) cc_final: 0.6973 (ttm110)
REVERT: c   46 ARG cc_start: 0.7092 (ptp-170) cc_final: 0.6663 (ptp90)
REVERT: c   63 ARG cc_start: 0.7777 (tmt-80) cc_final: 0.7518 (tmt-80)
REVERT: c   76 LEU cc_start: 0.7576 (mp) cc_final: 0.7291 (mp)
REVERT: c   96 MET cc_start: 0.6333 (tmm) cc_final: 0.6016 (tmm)
REVERT: c   97 TYR cc_start: 0.5959 (m-10) cc_final: 0.5249 (m-10)
REVERT: c  122 ILE cc_start: 0.8235 (tt) cc_final: 0.7923 (tt)
REVERT: c  184 LYS cc_start: 0.7402 (ptpp) cc_final: 0.6827 (ptpp)
REVERT: c  195 HIS cc_start: 0.6650 (m-70) cc_final: 0.6242 (m-70)
REVERT: c  260 GLN cc_start: 0.5709 (pm20) cc_final: 0.5393 (pm20)
REVERT: d    6 TYR cc_start: 0.6578 (m-80) cc_final: 0.6345 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 350
  average time/residue: 0.1259
  time to fit residues: 61.7925
Evaluate side-chains
  341 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 341
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 136 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0060
   chunk 35 optimal weight:    5.9990
   chunk 122 optimal weight:    0.7980
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.183717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.156478 restraints weight = 22381.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.162195 restraints weight = 13065.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.166214 restraints weight = 8549.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.169022 restraints weight = 6041.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.171121 restraints weight = 4541.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.4206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6140
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  13150  Z= 0.139
  Angle     :  0.756  15.081  17857  Z= 0.388
  Chirality :  0.049   0.454   1868
  Planarity :  0.005   0.076   2350
  Dihedral  :  6.048  42.350   1753
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 16.75 %
    Favored  : 82.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    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: -3.69 (0.21), residues: 1558
  helix: -0.45 (0.42), residues: 140
  sheet: -2.10 (0.24), residues: 447
  loop : -3.09 (0.19), residues: 971

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG c 167 
 TYR   0.026   0.001   TYR B  47 
 PHE   0.027   0.002   PHE A  73 
 TRP   0.034   0.002   TRP E  95 
 HIS   0.004   0.001   HIS c 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (13138)
  covalent geometry    : angle       0.75411 (17833)
  SS BOND              : bond        0.00571 (   12)
  SS BOND              : angle       1.52405 (   24)
  hydrogen bonds       : bond        0.03858 (  207)
  hydrogen bonds       : angle       6.60860 (  510)

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

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

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3116 Ramachandran restraints generated.
    1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 348
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLN cc_start: 0.7949 (pp30) cc_final: 0.7224 (pt0)
REVERT: A   63 GLU cc_start: 0.6855 (pm20) cc_final: 0.6438 (pm20)
REVERT: A   68 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8482 (mmmt)
REVERT: A  173 LYS cc_start: 0.8376 (ptpt) cc_final: 0.8173 (ptpt)
REVERT: B   62 PHE cc_start: 0.7320 (m-80) cc_final: 0.6890 (m-80)
REVERT: B   87 TYR cc_start: 0.6603 (m-80) cc_final: 0.5770 (m-80)
REVERT: B  192 LEU cc_start: 0.8035 (mm) cc_final: 0.7703 (mm)
REVERT: E   12 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7717 (mtt180)
REVERT: E   60 TRP cc_start: 0.6766 (m100) cc_final: 0.6516 (m100)
REVERT: E   96 ASP cc_start: 0.8138 (p0) cc_final: 0.7523 (p0)
REVERT: C    7 PHE cc_start: 0.6670 (m-10) cc_final: 0.6385 (m-10)
REVERT: C   19 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7985 (ttm110)
REVERT: C   46 ARG cc_start: 0.6860 (ptp90) cc_final: 0.6605 (ptp90)
REVERT: C  107 PHE cc_start: 0.8199 (t80) cc_final: 0.7956 (t80)
REVERT: D    8 LEU cc_start: 0.6693 (tt) cc_final: 0.6481 (tt)
REVERT: a   41 ARG cc_start: 0.6934 (ttt-90) cc_final: 0.6384 (ttt-90)
REVERT: a   63 GLU cc_start: 0.7052 (pm20) cc_final: 0.6777 (pm20)
REVERT: a   84 ASP cc_start: 0.8073 (m-30) cc_final: 0.7850 (m-30)
REVERT: a  111 LEU cc_start: 0.8415 (tp) cc_final: 0.8188 (tp)
REVERT: a  125 TYR cc_start: 0.6240 (m-80) cc_final: 0.6018 (m-80)
REVERT: b   93 LEU cc_start: 0.8548 (mt) cc_final: 0.8340 (mt)
REVERT: b  144 LEU cc_start: 0.8195 (mp) cc_final: 0.7922 (mp)
REVERT: e   58 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7663 (tmtt)
REVERT: c    7 PHE cc_start: 0.6574 (m-10) cc_final: 0.6097 (m-10)
REVERT: c   19 ARG cc_start: 0.7352 (ttm110) cc_final: 0.7095 (ttm110)
REVERT: c   46 ARG cc_start: 0.7120 (ptp-170) cc_final: 0.6704 (ptp90)
REVERT: c   76 LEU cc_start: 0.7446 (mp) cc_final: 0.7182 (mp)
REVERT: c   96 MET cc_start: 0.6376 (tmm) cc_final: 0.6087 (tmm)
REVERT: c   97 TYR cc_start: 0.5830 (m-10) cc_final: 0.5101 (m-10)
REVERT: c  122 ILE cc_start: 0.8127 (tt) cc_final: 0.7787 (tt)
REVERT: c  184 LYS cc_start: 0.7422 (ptpp) cc_final: 0.6848 (ptpp)
REVERT: c  195 HIS cc_start: 0.6618 (m-70) cc_final: 0.6245 (m-70)
REVERT: c  260 GLN cc_start: 0.5679 (pm20) cc_final: 0.5443 (pm20)
REVERT: d    6 TYR cc_start: 0.6592 (m-80) cc_final: 0.6329 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 348
  average time/residue: 0.1203
  time to fit residues: 59.0408
Evaluate side-chains
  340 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 340
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 133 optimal weight:    0.3980
   chunk 19 optimal weight:    5.9990
   chunk 65 optimal weight:    0.4980
   chunk 39 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 140 optimal weight:    4.9990
   chunk 123 optimal weight:    7.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
e  83 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.178175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.150684 restraints weight = 22470.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.156350 restraints weight = 13236.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.160366 restraints weight = 8716.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.163134 restraints weight = 6194.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.164980 restraints weight = 4675.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6263
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13150  Z= 0.237
  Angle     :  0.825  12.887  17857  Z= 0.428
  Chirality :  0.052   0.413   1868
  Planarity :  0.006   0.071   2350
  Dihedral  :  6.555  42.814   1753
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 20.15 %
    Favored  : 79.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.41 %
    Twisted General : 0.07 %

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: -3.82 (0.20), residues: 1558
  helix: -0.63 (0.43), residues: 140
  sheet: -2.32 (0.24), residues: 431
  loop : -3.10 (0.19), residues: 987

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG c 167 
 TYR   0.022   0.002   TYR E  10 
 PHE   0.039   0.002   PHE E  30 
 TRP   0.030   0.003   TRP e  60 
 HIS   0.005   0.001   HIS c  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (13138)
  covalent geometry    : angle       0.82349 (17833)
  SS BOND              : bond        0.00894 (   12)
  SS BOND              : angle       1.75137 (   24)
  hydrogen bonds       : bond        0.04556 (  207)
  hydrogen bonds       : angle       7.07923 (  510)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2486.14 seconds
wall clock time: 43 minutes 49.22 seconds (2629.22 seconds total)