Starting phenix.real_space_refine
on Thu Mar 13 09:27:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wyb_32890/03_2025/7wyb_32890_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wyb_32890/03_2025/7wyb_32890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wyb_32890/03_2025/7wyb_32890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wyb_32890/03_2025/7wyb_32890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wyb_32890/03_2025/7wyb_32890_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wyb_32890/03_2025/7wyb_32890_neut.cif"
  }
  resolution = 2.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
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      66      5.16       5
     C    5587      2.51       5
     N    1476      2.21       5
     O    1628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8757
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 1812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1812
          Classifications: {'peptide': 226}
          Link IDs: {'PTRANS': 2, 'TRANS': 223}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2607
          Classifications: {'peptide': 339}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
    Chain: "D"
      Number of atoms: 444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 444
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "E"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1771
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 262, 2123
          Classifications: {'peptide': 262}
          Link IDs: {'PTRANS': 3, 'TRANS': 258}
          Chain breaks: 1
  Time building chain proxies: 5.35, per 1000 atoms: 0.61
  Number of scatterers: 8757
  At special positions: 0
  Unit cell: (92.4, 122.1, 130.9, 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      66     16.00
     O    1628      8.00
     N    1476      7.00
     C    5587      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 161 " - pdb=" SG  CYS E 231 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R1008 " - pdb=" SG  CYS R1080 " 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: 2.47
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2080

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      35.3% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 30
      removed outlier: 3.551A  pdb=" N   ALA B  12 " --> pdb=" O   GLU B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 54
    Processing helix  chain 'B' and resid 207 through 212
      removed outlier: 4.407A  pdb=" N   TRP B 211 " --> pdb=" O   GLU B 207 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ILE B 212 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 207 through 212'
    Processing helix  chain 'B' and resid 213 through 216
      removed outlier: 3.736A  pdb=" N   GLU B 216 " --> pdb=" O   HIS B 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 213 through 216'
    Processing helix  chain 'B' and resid 241 through 255
      removed outlier: 3.842A  pdb=" N   ALA B 245 " --> pdb=" O   ASN B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 260
      removed outlier: 3.777A  pdb=" N   PHE B 259 " --> pdb=" O   ASN B 256 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR B 260 " --> pdb=" O   LYS B 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 256 through 260'
    Processing helix  chain 'B' and resid 271 through 279
    Processing helix  chain 'B' and resid 295 through 309
      removed outlier: 3.654A  pdb=" N   ALA B 299 " --> pdb=" O   THR B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 331
    Processing helix  chain 'B' and resid 332 through 348
    Processing helix  chain 'C' and resid 3 through 26
      removed outlier: 3.774A  pdb=" N   ALA C  26 " --> pdb=" O   ARG C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 33
    Processing helix  chain 'D' and resid 6 through 24
    Processing helix  chain 'D' and resid 29 through 43
    Processing helix  chain 'D' and resid 44 through 48
      removed outlier: 3.521A  pdb=" N   GLU D  47 " --> pdb=" O   HIS D  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.957A  pdb=" N   SER E  31 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE E  32 " --> pdb=" O   PHE E  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 28 through 32'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.034A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 924 through 929
    Processing helix  chain 'R' and resid 940 through 956
    Processing helix  chain 'R' and resid 958 through 970
      removed outlier: 3.821A  pdb=" N   ILE R 962 " --> pdb=" O   VAL R 958 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE R 970 " --> pdb=" O   THR R 966 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 971 through 974
      removed outlier: 3.656A  pdb=" N   GLN R 974 " --> pdb=" O   ARG R 971 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 971 through 974'
    Processing helix  chain 'R' and resid 975 through 999
      removed outlier: 3.597A  pdb=" N   ILE R 999 " --> pdb=" O   PHE R 995 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1007 through 1038
      removed outlier: 3.930A  pdb=" N   PHE R1011 " --> pdb=" O   ALA R1007 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1047 through 1070
      removed outlier: 3.762A  pdb=" N   PHE R1051 " --> pdb=" O   ARG R1047 " (cutoff:3.500A)
      Proline residue:  R1059  - end of helix
    Processing helix  chain 'R' and resid 1088 through 1091
    Processing helix  chain 'R' and resid 1092 through 1099
      removed outlier: 3.658A  pdb=" N   ALA R1096 " --> pdb=" O   PHE R1092 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1099 through 1117
      removed outlier: 4.131A  pdb=" N   ILE R1105 " --> pdb=" O   MET R1101 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1144 through 1154
      removed outlier: 3.652A  pdb=" N   CYS R1152 " --> pdb=" O   ILE R1148 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   LEU R1153 " --> pdb=" O   ALA R1149 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU R1154 " --> pdb=" O   LEU R1150 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1155 through 1162
    Processing helix  chain 'R' and resid 1169 through 1181
      removed outlier: 3.801A  pdb=" N   ALA R1173 " --> pdb=" O   THR R1169 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1182 through 1193
      removed outlier: 4.024A  pdb=" N   VAL R1193 " --> pdb=" O   ILE R1189 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1195 through 1206
    Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191
      removed outlier: 6.355A  pdb=" N   VAL B  34 " --> pdb=" O   LYS B 197 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   PHE B 199 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU B  36 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ALA B 220 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   ILE B 264 " --> pdb=" O   TYR B 320 " (cutoff:3.500A)
      removed outlier: 8.483A  pdb=" N   HIS B 322 " --> pdb=" O   ILE B 264 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LEU B 266 " --> pdb=" O   HIS B 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 7.155A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.827A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.808A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 7.284A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.465A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG C 137 " --> pdb=" O   ILE C 123 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153
      removed outlier: 3.807A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLN C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER C 161 " --> pdb=" O   THR C 165 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191
      removed outlier: 6.829A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277
      removed outlier: 3.691A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 6.545A  pdb=" N   GLY E  16 " --> pdb=" O   SER E  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.739A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.335A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 142 through 144
    Processing sheet with id=AB3, first strand: chain 'E' and resid 149 through 150
      removed outlier: 3.898A  pdb=" N   GLU E 248 " --> pdb=" O   VAL E 149 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   LEU E 180 " --> pdb=" O   LEU E 189 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   LEU E 189 " --> pdb=" O   LEU E 180 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   TYR E 192 " --> pdb=" O   ASN E 196 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ASN E 196 " --> pdb=" O   TYR E 192 " (cutoff:3.500A)

    402 hydrogen bonds defined for protein.
    1104 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: 2.79

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2808
        1.35 -     1.47: 2259
        1.47 -     1.59: 3778
        1.59 -     1.71: 0
        1.71 -     1.83: 96
  Bond restraints: 8941
  Sorted by residual:
  bond pdb=" N   THR E 212 "
       pdb=" CA  THR E 212 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.32e-02 5.74e+03 7.61e+00
  bond pdb=" N   GLU E 236 "
       pdb=" CA  GLU E 236 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.032 1.18e-02 7.18e+03 7.46e+00
  bond pdb=" CA  ALA C 299 "
       pdb=" C   ALA C 299 "
    ideal  model  delta    sigma   weight residual
    1.523  1.479  0.044 1.80e-02 3.09e+03 6.01e+00
  bond pdb=" N   TYR E 237 "
       pdb=" CA  TYR E 237 "
    ideal  model  delta    sigma   weight residual
    1.452  1.487 -0.035 1.41e-02 5.03e+03 5.99e+00
  bond pdb=" C   GLN C  44 "
       pdb=" N   MET C  45 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.31e-02 5.83e+03 5.87e+00
  ... (remaining 8936 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 11676
        1.90 -     3.80: 345
        3.80 -     5.70: 64
        5.70 -     7.59: 11
        7.59 -     9.49: 3
  Bond angle restraints: 12099
  Sorted by residual:
  angle pdb=" N   SER R1168 "
        pdb=" CA  SER R1168 "
        pdb=" C   SER R1168 "
      ideal   model   delta    sigma   weight residual
     113.23  107.67    5.56 1.22e+00 6.72e-01 2.08e+01
  angle pdb=" N   LYS B 349 "
        pdb=" CA  LYS B 349 "
        pdb=" C   LYS B 349 "
      ideal   model   delta    sigma   weight residual
     114.04  108.94    5.10 1.24e+00 6.50e-01 1.69e+01
  angle pdb=" C   PRO E  14 "
        pdb=" CA  PRO E  14 "
        pdb=" CB  PRO E  14 "
      ideal   model   delta    sigma   weight residual
     111.39  116.45   -5.06 1.28e+00 6.10e-01 1.57e+01
  angle pdb=" N   PHE R 970 "
        pdb=" CA  PHE R 970 "
        pdb=" C   PHE R 970 "
      ideal   model   delta    sigma   weight residual
     109.15  114.77   -5.62 1.44e+00 4.82e-01 1.52e+01
  angle pdb=" C   LEU C  55 "
        pdb=" CA  LEU C  55 "
        pdb=" CB  LEU C  55 "
      ideal   model   delta    sigma   weight residual
     109.65  103.09    6.56 1.68e+00 3.54e-01 1.52e+01
  ... (remaining 12094 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 4853
       17.55 -    35.10: 360
       35.10 -    52.65: 52
       52.65 -    70.20: 3
       70.20 -    87.75: 6
  Dihedral angle restraints: 5274
    sinusoidal: 2047
      harmonic: 3227
  Sorted by residual:
  dihedral pdb=" CB  CYS E 161 "
           pdb=" SG  CYS E 161 "
           pdb=" SG  CYS E 231 "
           pdb=" CB  CYS E 231 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  135.64  -42.64     1      1.00e+01 1.00e-02 2.54e+01
  dihedral pdb=" CB  CYS R1008 "
           pdb=" SG  CYS R1008 "
           pdb=" SG  CYS R1080 "
           pdb=" CB  CYS R1080 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -47.47  -38.53     1      1.00e+01 1.00e-02 2.09e+01
  dihedral pdb=" CA  ARG E 193 "
           pdb=" C   ARG E 193 "
           pdb=" N   MET E 194 "
           pdb=" CA  MET E 194 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.55   19.45     0      5.00e+00 4.00e-02 1.51e+01
  ... (remaining 5271 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1023
       0.051 -    0.102: 282
       0.102 -    0.153: 56
       0.153 -    0.204: 6
       0.204 -    0.255: 2
  Chirality restraints: 1369
  Sorted by residual:
  chirality pdb=" CA  LEU R 928 "
            pdb=" N   LEU R 928 "
            pdb=" C   LEU R 928 "
            pdb=" CB  LEU R 928 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  GLU B 216 "
            pdb=" N   GLU B 216 "
            pdb=" C   GLU B 216 "
            pdb=" CB  GLU B 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  ALA C  56 "
            pdb=" N   ALA C  56 "
            pdb=" C   ALA C  56 "
            pdb=" CB  ALA C  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.68   -0.20 2.00e-01 2.50e+01 9.81e-01
  ... (remaining 1366 not shown)

  Planarity restraints: 1525
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG E 182 "   -0.050 5.00e-02 4.00e+02   7.57e-02 9.18e+00
        pdb=" N   PRO E 183 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO E 183 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO E 183 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 210 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.53e+00
        pdb=" C   SER E 210 "    0.032 2.00e-02 2.50e+03
        pdb=" O   SER E 210 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY E 211 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 222 "   -0.007 2.00e-02 2.50e+03   1.37e-02 3.29e+00
        pdb=" CG  PHE C 222 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 222 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 222 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 222 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 222 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 222 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1522 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 447
        2.72 -     3.27: 8475
        3.27 -     3.81: 13324
        3.81 -     4.36: 16117
        4.36 -     4.90: 28133
  Nonbonded interactions: 66496
  Sorted by model distance:
  nonbonded pdb=" O   GLY E 211 "
            pdb=" OG1 THR E 212 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" OG1 THR C 274 "
            pdb=" O   VAL C 315 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   ALA B  41 "
            pdb=" OG  SER B  44 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   GLU R1167 "
            pdb=" OG  SER R1168 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ARG C 314 "
            pdb=" OG  SER C 331 "
     model   vdw
     2.293 3.040
  ... (remaining 66491 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.750
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:17.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5858
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      :  0.005   0.053   8941  Z= 0.354
  Angle     :  0.803   9.493  12099  Z= 0.464
  Chirality :  0.049   0.255   1369
  Planarity :  0.005   0.076   1525
  Dihedral  : 12.351  87.746   3188
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.25), residues: 1099
  helix:  0.32 (0.29), residues: 348
  sheet: -0.19 (0.32), residues: 276
  loop : -2.27 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C  82 
 HIS   0.008   0.001   HIS R1016 
 PHE   0.028   0.003   PHE C 222 
 TYR   0.031   0.002   TYR C 105 
 ARG   0.006   0.000   ARG C 304 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.846 
Fit side-chains
REVERT: B  308 GLU cc_start: 0.6288 (mt-10) cc_final: 0.6083 (mt-10)
REVERT: C  101 MET cc_start: 0.5505 (mtt) cc_final: 0.5283 (ttm)
REVERT: E  246 LYS cc_start: 0.7146 (ttmm) cc_final: 0.6845 (ttmm)
REVERT: R 1180 ASN cc_start: 0.7186 (m-40) cc_final: 0.6938 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 1.1203
  time to fit residues: 141.7894
Evaluate side-chains
  105 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:    0.0570
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
B 255 ASN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 233 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.190189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.161691 restraints weight = 12042.560|
|-----------------------------------------------------------------------------|
r_work (start): 0.4298 rms_B_bonded: 2.90
r_work: 0.4177 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6053
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8941  Z= 0.240
  Angle     :  0.635   9.867  12099  Z= 0.338
  Chirality :  0.043   0.194   1369
  Planarity :  0.004   0.056   1525
  Dihedral  :  5.248  46.413   1201
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  8.19 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.25), residues: 1099
  helix:  0.75 (0.29), residues: 348
  sheet:  0.12 (0.32), residues: 275
  loop : -1.98 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 211 
 HIS   0.005   0.001   HIS R1016 
 PHE   0.018   0.002   PHE C 253 
 TYR   0.021   0.002   TYR C 105 
 ARG   0.004   0.000   ARG E  72 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 2.178 
Fit side-chains
   revert: symmetry clash
REVERT: B  240 MET cc_start: 0.5713 (tmm) cc_final: 0.5196 (pp-130)
REVERT: C   52 ARG cc_start: 0.7346 (mtt90) cc_final: 0.7112 (mtt90)
REVERT: C  101 MET cc_start: 0.6225 (mtt) cc_final: 0.5817 (tpt)
REVERT: C  219 ARG cc_start: 0.7189 (tpt-90) cc_final: 0.6952 (tpt-90)
REVERT: C  239 ASN cc_start: 0.6966 (m-40) cc_final: 0.6268 (t0)
REVERT: D   21 MET cc_start: 0.0124 (mtm) cc_final: -0.0372 (mtm)
REVERT: E   76 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6746 (mtpp)
REVERT: E  246 LYS cc_start: 0.7087 (ttmm) cc_final: 0.6778 (ttmm)
REVERT: R 1114 MET cc_start: 0.6884 (tpp) cc_final: 0.6544 (tmm)
  outliers start: 15
  outliers final: 6
  residues processed: 115
  average time/residue: 1.5468
  time to fit residues: 191.4952
Evaluate side-chains
  114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 61 optimal weight:    0.1980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
B 255 ASN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** 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 = 0.4572 r_free = 0.4572 target = 0.189183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.160621 restraints weight = 12196.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.4285 rms_B_bonded: 2.92
r_work: 0.4161 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6077
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8941  Z= 0.258
  Angle     :  0.614  10.163  12099  Z= 0.328
  Chirality :  0.043   0.222   1369
  Planarity :  0.004   0.049   1525
  Dihedral  :  5.106  45.606   1201
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 10.82 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.25), residues: 1099
  helix:  0.81 (0.29), residues: 354
  sheet:  0.12 (0.31), residues: 295
  loop : -1.89 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 211 
 HIS   0.006   0.001   HIS R1016 
 PHE   0.018   0.002   PHE C 253 
 TYR   0.025   0.002   TYR C 105 
 ARG   0.003   0.000   ARG E  72 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5208 (ppp)
REVERT: B  309 ASP cc_start: 0.5747 (m-30) cc_final: 0.5468 (m-30)
REVERT: C   52 ARG cc_start: 0.7318 (mtt90) cc_final: 0.7087 (mtt90)
REVERT: C  101 MET cc_start: 0.6257 (mtt) cc_final: 0.5690 (tpt)
REVERT: C  219 ARG cc_start: 0.7128 (tpt-90) cc_final: 0.6877 (tpt-90)
REVERT: C  239 ASN cc_start: 0.6932 (m-40) cc_final: 0.6264 (t0)
REVERT: D   21 MET cc_start: 0.0049 (mtm) cc_final: -0.0435 (mtm)
REVERT: E   76 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6764 (mtpp)
REVERT: E  246 LYS cc_start: 0.7019 (ttmm) cc_final: 0.6738 (ttmm)
REVERT: R  945 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5837 (mp)
REVERT: R 1114 MET cc_start: 0.6997 (tpp) cc_final: 0.6770 (tmm)
  outliers start: 22
  outliers final: 12
  residues processed: 116
  average time/residue: 1.0786
  time to fit residues: 134.6804
Evaluate side-chains
  120 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 MET
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  211 TRP
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain E residue  232 MET
Chi-restraints excluded: chain R residue  945 LEU
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1079 VAL
Chi-restraints excluded: chain R residue 1109 ILE
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0040
   chunk 106 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   chunk 44 optimal weight:    0.1980
   chunk 56 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
B 255 ASN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** 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 = 0.4588 r_free = 0.4588 target = 0.190584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.162235 restraints weight = 12086.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.4308 rms_B_bonded: 2.88
r_work: 0.4185 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6026
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8941  Z= 0.201
  Angle     :  0.578  10.626  12099  Z= 0.306
  Chirality :  0.041   0.153   1369
  Planarity :  0.003   0.045   1525
  Dihedral  :  4.833  43.426   1201
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.92 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.25), residues: 1099
  helix:  1.19 (0.29), residues: 347
  sheet:  0.20 (0.32), residues: 284
  loop : -1.80 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 211 
 HIS   0.004   0.001   HIS R1016 
 PHE   0.015   0.002   PHE C 253 
 TYR   0.017   0.002   TYR C 105 
 ARG   0.002   0.000   ARG E  72 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.5812 (ppp) cc_final: 0.5193 (ppp)
REVERT: C   52 ARG cc_start: 0.7285 (mtt90) cc_final: 0.7046 (mtt90)
REVERT: C  101 MET cc_start: 0.6200 (mtt) cc_final: 0.5925 (mtm)
REVERT: C  219 ARG cc_start: 0.7032 (tpt-90) cc_final: 0.6773 (tpt-90)
REVERT: C  239 ASN cc_start: 0.6828 (m-40) cc_final: 0.6232 (t0)
REVERT: D   21 MET cc_start: 0.0077 (mtm) cc_final: -0.0377 (mtm)
REVERT: E   62 ASP cc_start: 0.6979 (OUTLIER) cc_final: 0.6533 (m-30)
REVERT: E   76 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6690 (mtpp)
REVERT: E  246 LYS cc_start: 0.6966 (ttmm) cc_final: 0.6687 (ttmm)
REVERT: R  945 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5822 (mp)
REVERT: R 1114 MET cc_start: 0.7036 (tpp) cc_final: 0.6836 (tmm)
  outliers start: 20
  outliers final: 8
  residues processed: 121
  average time/residue: 1.0191
  time to fit residues: 132.9516
Evaluate side-chains
  118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain C residue  211 TRP
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain R residue  945 LEU
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    0.2980
   chunk 39 optimal weight:    0.4980
   chunk 102 optimal weight:    0.0970
   chunk 37 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 234 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.192052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.163567 restraints weight = 12128.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.4318 rms_B_bonded: 2.93
r_work: 0.4192 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6023
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8941  Z= 0.186
  Angle     :  0.556   9.906  12099  Z= 0.295
  Chirality :  0.041   0.156   1369
  Planarity :  0.003   0.041   1525
  Dihedral  :  4.622  42.454   1201
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.45 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.26), residues: 1099
  helix:  1.54 (0.30), residues: 339
  sheet:  0.19 (0.32), residues: 289
  loop : -1.68 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 211 
 HIS   0.004   0.001   HIS R1016 
 PHE   0.017   0.002   PHE C 241 
 TYR   0.015   0.001   TYR C 105 
 ARG   0.002   0.000   ARG C 304 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.5595 (ppp) cc_final: 0.5008 (ppp)
REVERT: B  198 MET cc_start: 0.7316 (mtp) cc_final: 0.6679 (mtt)
REVERT: B  309 ASP cc_start: 0.5697 (m-30) cc_final: 0.5307 (m-30)
REVERT: C  101 MET cc_start: 0.6176 (mtt) cc_final: 0.5918 (mtm)
REVERT: C  239 ASN cc_start: 0.6836 (m-40) cc_final: 0.6260 (t0)
REVERT: D   21 MET cc_start: 0.0097 (mtm) cc_final: -0.0336 (mtm)
REVERT: E  246 LYS cc_start: 0.6927 (ttmm) cc_final: 0.6726 (ttmm)
  outliers start: 22
  outliers final: 17
  residues processed: 120
  average time/residue: 1.0222
  time to fit residues: 132.9548
Evaluate side-chains
  123 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  211 TRP
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain E residue  212 THR
Chi-restraints excluded: chain E residue  232 MET
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1079 VAL
Chi-restraints excluded: chain R residue 1109 ILE
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0040
   chunk 79 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 234 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.190758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.161921 restraints weight = 12049.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.4303 rms_B_bonded: 2.92
r_work: 0.4181 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6049
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8941  Z= 0.229
  Angle     :  0.601   9.560  12099  Z= 0.313
  Chirality :  0.042   0.195   1369
  Planarity :  0.003   0.041   1525
  Dihedral  :  4.699  43.332   1201
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 15.23 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.26), residues: 1099
  helix:  1.49 (0.29), residues: 339
  sheet:  0.10 (0.31), residues: 289
  loop : -1.66 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP R1143 
 HIS   0.006   0.001   HIS R1016 
 PHE   0.018   0.002   PHE B 199 
 TYR   0.018   0.002   TYR C 105 
 ARG   0.002   0.000   ARG E  72 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.5504 (ppp) cc_final: 0.4955 (pp-130)
REVERT: B  198 MET cc_start: 0.7258 (mtp) cc_final: 0.6613 (mtt)
REVERT: C  101 MET cc_start: 0.6142 (mtt) cc_final: 0.5872 (ttm)
REVERT: C  239 ASN cc_start: 0.6840 (m-40) cc_final: 0.6193 (t0)
REVERT: D   21 MET cc_start: 0.0064 (mtm) cc_final: -0.0366 (mtm)
REVERT: E   76 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6778 (mtpp)
  outliers start: 29
  outliers final: 19
  residues processed: 122
  average time/residue: 1.0398
  time to fit residues: 137.3300
Evaluate side-chains
  125 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  211 TRP
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain E residue  212 THR
Chi-restraints excluded: chain E residue  222 GLU
Chi-restraints excluded: chain E residue  232 MET
Chi-restraints excluded: chain R residue  928 LEU
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1079 VAL
Chi-restraints excluded: chain R residue 1109 ILE
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 90 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 234 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.190113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.161517 restraints weight = 12136.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.4298 rms_B_bonded: 2.87
r_work: 0.4178 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6055
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8941  Z= 0.247
  Angle     :  0.609  10.599  12099  Z= 0.318
  Chirality :  0.042   0.186   1369
  Planarity :  0.003   0.040   1525
  Dihedral  :  4.769  43.102   1201
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.76 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.26), residues: 1099
  helix:  1.19 (0.29), residues: 353
  sheet:  0.01 (0.31), residues: 289
  loop : -1.67 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 211 
 HIS   0.006   0.001   HIS R1016 
 PHE   0.018   0.002   PHE C 241 
 TYR   0.018   0.002   TYR C 105 
 ARG   0.002   0.000   ARG E  72 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.5473 (ppp) cc_final: 0.4984 (pp-130)
REVERT: B  198 MET cc_start: 0.7309 (mtp) cc_final: 0.6690 (mtt)
REVERT: B  309 ASP cc_start: 0.5724 (m-30) cc_final: 0.5337 (m-30)
REVERT: C  101 MET cc_start: 0.6170 (mtt) cc_final: 0.5876 (ttm)
REVERT: C  239 ASN cc_start: 0.6840 (m-40) cc_final: 0.6181 (t0)
REVERT: D   21 MET cc_start: 0.0224 (mtm) cc_final: -0.0227 (mtm)
REVERT: E   76 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6810 (mtpp)
  outliers start: 27
  outliers final: 18
  residues processed: 119
  average time/residue: 1.0091
  time to fit residues: 130.0029
Evaluate side-chains
  123 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  211 TRP
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain E residue  212 THR
Chi-restraints excluded: chain E residue  222 GLU
Chi-restraints excluded: chain E residue  232 MET
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1079 VAL
Chi-restraints excluded: chain R residue 1109 ILE
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 73 optimal weight:    0.0020
   chunk 67 optimal weight:    0.8980
   chunk 55 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 87 optimal weight:    0.0970
   chunk 92 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   chunk 105 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
C  75 GLN
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  18 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.193391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.164531 restraints weight = 12355.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.4331 rms_B_bonded: 2.92
r_work: 0.4211 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.4211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5995
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8941  Z= 0.168
  Angle     :  0.565  10.504  12099  Z= 0.293
  Chirality :  0.040   0.149   1369
  Planarity :  0.003   0.039   1525
  Dihedral  :  4.411  41.469   1201
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.65 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.26), residues: 1099
  helix:  1.70 (0.29), residues: 340
  sheet:  0.03 (0.31), residues: 288
  loop : -1.56 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 211 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.013   0.001   PHE C 151 
 TYR   0.019   0.001   TYR R1112 
 ARG   0.002   0.000   ARG E  72 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.5462 (ppp) cc_final: 0.4915 (pp-130)
REVERT: B  198 MET cc_start: 0.7166 (mtp) cc_final: 0.6514 (mtt)
REVERT: C  101 MET cc_start: 0.6127 (mtt) cc_final: 0.5869 (mtm)
REVERT: C  239 ASN cc_start: 0.6785 (m-40) cc_final: 0.6159 (t0)
REVERT: D   21 MET cc_start: 0.0254 (mtm) cc_final: -0.0177 (mtm)
  outliers start: 18
  outliers final: 12
  residues processed: 112
  average time/residue: 1.0526
  time to fit residues: 127.4020
Evaluate side-chains
  110 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain C residue  211 TRP
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  212 THR
Chi-restraints excluded: chain E residue  222 GLU
Chi-restraints excluded: chain E residue  232 MET
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1079 VAL
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0970
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0570
   chunk 32 optimal weight:    0.7980
   chunk 106 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** 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 = 0.4618 r_free = 0.4618 target = 0.193387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.164432 restraints weight = 12208.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.4323 rms_B_bonded: 2.96
r_work: 0.4201 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6003
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8941  Z= 0.185
  Angle     :  0.576  11.630  12099  Z= 0.299
  Chirality :  0.041   0.141   1369
  Planarity :  0.003   0.039   1525
  Dihedral  :  4.407  42.083   1201
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 18.59 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.26), residues: 1099
  helix:  1.74 (0.29), residues: 340
  sheet: -0.03 (0.31), residues: 288
  loop : -1.47 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R1081 
 HIS   0.004   0.001   HIS R1016 
 PHE   0.019   0.002   PHE C 241 
 TYR   0.013   0.001   TYR C 105 
 ARG   0.002   0.000   ARG E  72 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.5495 (ppp) cc_final: 0.4947 (pp-130)
REVERT: B  198 MET cc_start: 0.7175 (mtp) cc_final: 0.6506 (mtt)
REVERT: C  101 MET cc_start: 0.6125 (mtt) cc_final: 0.5864 (ttm)
REVERT: C  239 ASN cc_start: 0.6764 (m-40) cc_final: 0.6099 (t0)
REVERT: D   21 MET cc_start: 0.0205 (mtm) cc_final: -0.0218 (mtm)
  outliers start: 16
  outliers final: 14
  residues processed: 108
  average time/residue: 1.0929
  time to fit residues: 127.3858
Evaluate side-chains
  113 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain C residue   72 SER
Chi-restraints excluded: chain C residue  211 TRP
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue  212 THR
Chi-restraints excluded: chain E residue  222 GLU
Chi-restraints excluded: chain E residue  232 MET
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 98 optimal weight:    0.3980
   chunk 105 optimal weight:    0.0170
   chunk 95 optimal weight:    0.8980
   chunk 56 optimal weight:    7.9990
   chunk 100 optimal weight:    0.0000
   chunk 78 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   overall best weight:    0.3222

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

Flipped N/Q/H residues before XYZ refinement:
B 213 HIS
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** 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 = 0.4630 r_free = 0.4630 target = 0.194560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.165727 restraints weight = 12165.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.4335 rms_B_bonded: 2.95
r_work: 0.4213 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5978
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8941  Z= 0.170
  Angle     :  0.571  11.183  12099  Z= 0.295
  Chirality :  0.040   0.144   1369
  Planarity :  0.003   0.039   1525
  Dihedral  :  4.314  41.244   1201
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 18.59 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.26), residues: 1099
  helix:  1.68 (0.29), residues: 347
  sheet:  0.01 (0.31), residues: 289
  loop : -1.41 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 211 
 HIS   0.003   0.001   HIS R1016 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.020   0.001   TYR R1112 
 ARG   0.004   0.000   ARG E  67 

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

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

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2198 Ramachandran restraints generated.
    1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 MET cc_start: 0.5479 (ppp) cc_final: 0.4919 (pp-130)
REVERT: B  198 MET cc_start: 0.7156 (mtp) cc_final: 0.6472 (mtt)
REVERT: C  101 MET cc_start: 0.6103 (mtt) cc_final: 0.5854 (ttm)
REVERT: C  239 ASN cc_start: 0.6726 (m-40) cc_final: 0.6161 (t0)
REVERT: D   21 MET cc_start: 0.0214 (mtm) cc_final: -0.0197 (mtm)
  outliers start: 14
  outliers final: 10
  residues processed: 108
  average time/residue: 1.1539
  time to fit residues: 134.0513
Evaluate side-chains
  110 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue  247 MET
Chi-restraints excluded: chain B residue  307 PHE
Chi-restraints excluded: chain C residue  211 TRP
Chi-restraints excluded: chain C residue  300 LEU
Chi-restraints excluded: chain E residue  174 THR
Chi-restraints excluded: chain E residue  212 THR
Chi-restraints excluded: chain E residue  222 GLU
Chi-restraints excluded: chain R residue 1058 MET
Chi-restraints excluded: chain R residue 1178 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 103 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0020
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 340 ASN ** 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 = 0.4612 r_free = 0.4612 target = 0.192692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.163888 restraints weight = 12225.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.4320 rms_B_bonded: 2.95
r_work: 0.4197 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8941  Z= 0.208
  Angle     :  0.593  13.006  12099  Z= 0.307
  Chirality :  0.041   0.142   1369
  Planarity :  0.003   0.038   1525
  Dihedral  :  4.477  42.703   1201
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.91 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.26), residues: 1099
  helix:  1.57 (0.29), residues: 348
  sheet: -0.01 (0.31), residues: 288
  loop : -1.43 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 211 
 HIS   0.006   0.001   HIS R1016 
 PHE   0.019   0.002   PHE C 241 
 TYR   0.015   0.001   TYR C 105 
 ARG   0.002   0.000   ARG C 314 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7183.26 seconds
wall clock time: 124 minutes 58.42 seconds (7498.42 seconds total)