Starting phenix.real_space_refine
on Mon Jul 28 14:53:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xos_38539/07_2025/8xos_38539.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xos_38539/07_2025/8xos_38539.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xos_38539/07_2025/8xos_38539.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xos_38539/07_2025/8xos_38539.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xos_38539/07_2025/8xos_38539.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xos_38539/07_2025/8xos_38539.cif"
  }
  resolution = 3.2
  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=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1946 atoms to isotropic.
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      65      5.16       5
     C    5713      2.51       5
     N    1476      2.21       5
     O    1665      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8919
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1752
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2577
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2577
          Classifications: {'peptide': 336}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "E"
      Number of atoms: 1781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1781
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2335
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 11, 'TRANS': 285}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.63, per 1000 atoms: 0.63
  Number of scatterers: 8919
  At special positions: 0
  Unit cell: (116.739, 94.248, 117.81, 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      65     16.00
     O    1665      8.00
     N    1476      7.00
     C    5713      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 175 " - pdb=" SG  CYS R 254 " 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: 2.39
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2134

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 14 sheets defined
      38.4% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.511A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 52
    Processing helix  chain 'A' and resid 207 through 218
      removed outlier: 4.707A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   GLY A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.434A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 7 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.504A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
    Processing helix  chain 'E' and resid 74 through 76
      No H-bonds generated for 'chain 'E' and resid 74 through 76'
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'E' and resid 220 through 224
    Processing helix  chain 'R' and resid 89 through 98
    Processing helix  chain 'R' and resid 103 through 127
      Proline residue:  R 118  - end of helix
    Processing helix  chain 'R' and resid 135 through 154
      removed outlier: 3.553A  pdb=" N   VAL R 154 " --> pdb=" O   LEU R 150 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 164
      removed outlier: 3.872A  pdb=" N   LYS R 158 " --> pdb=" O   VAL R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 206
    Processing helix  chain 'R' and resid 206 through 214
      removed outlier: 3.618A  pdb=" N   LEU R 211 " --> pdb=" O   PRO R 207 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   SER R 212 " --> pdb=" O   MET R 208 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 215 through 234
      removed outlier: 3.653A  pdb=" N   VAL R 234 " --> pdb=" O   ALA R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 234 through 240
    Processing helix  chain 'R' and resid 260 through 266
    Processing helix  chain 'R' and resid 266 through 279
    Processing helix  chain 'R' and resid 279 through 298
    Processing helix  chain 'R' and resid 308 through 325
    Processing helix  chain 'R' and resid 326 through 337
    Processing helix  chain 'R' and resid 342 through 361
      removed outlier: 4.407A  pdb=" N   GLU R 347 " --> pdb=" O   THR R 343 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   ALA R 348 " --> pdb=" O   SER R 344 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 362 through 372
      Proline residue:  R 368  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 9.071A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.772A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.531A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.578A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.916A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.543A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.843A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.427A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.686A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASP B 254 " --> pdb=" O   GLN B 259 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.772A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.513A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.513A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.152A  pdb=" N   VAL E 147 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 87 through 88

    446 hydrogen bonds defined for protein.
    1224 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: 3.04

  Time building geometry restraints manager: 2.81 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: 2817
        1.34 -     1.46: 2032
        1.46 -     1.58: 4174
        1.58 -     1.70: 0
        1.70 -     1.82: 91
  Bond restraints: 9114
  Sorted by residual:
  bond pdb=" CD2 HIS E 232 "
       pdb=" NE2 HIS E 232 "
    ideal  model  delta    sigma   weight residual
    1.374  1.397 -0.023 1.10e-02 8.26e+03 4.40e+00
  bond pdb=" N   SER A   6 "
       pdb=" CA  SER A   6 "
    ideal  model  delta    sigma   weight residual
    1.455  1.479 -0.024 1.27e-02 6.20e+03 3.62e+00
  bond pdb=" C13 CLR R 601 "
       pdb=" C17 CLR R 601 "
    ideal  model  delta    sigma   weight residual
    1.550  1.513  0.037 2.00e-02 2.50e+03 3.48e+00
  bond pdb=" C13 CLR R 602 "
       pdb=" C17 CLR R 602 "
    ideal  model  delta    sigma   weight residual
    1.550  1.514  0.036 2.00e-02 2.50e+03 3.27e+00
  bond pdb=" CE1 HIS E 232 "
       pdb=" NE2 HIS E 232 "
    ideal  model  delta    sigma   weight residual
    1.321  1.339 -0.018 1.00e-02 1.00e+04 3.22e+00
  ... (remaining 9109 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 11435
        1.58 -     3.16: 786
        3.16 -     4.73: 111
        4.73 -     6.31: 18
        6.31 -     7.89: 10
  Bond angle restraints: 12360
  Sorted by residual:
  angle pdb=" CB  HIS E  35 "
        pdb=" CG  HIS E  35 "
        pdb=" CD2 HIS E  35 "
      ideal   model   delta    sigma   weight residual
     131.20  125.42    5.78 1.30e+00 5.92e-01 1.98e+01
  angle pdb=" CB  HIS E 167 "
        pdb=" CG  HIS E 167 "
        pdb=" CD2 HIS E 167 "
      ideal   model   delta    sigma   weight residual
     131.20  125.62    5.58 1.30e+00 5.92e-01 1.84e+01
  angle pdb=" CB  HIS E 232 "
        pdb=" CG  HIS E 232 "
        pdb=" CD2 HIS E 232 "
      ideal   model   delta    sigma   weight residual
     131.20  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  angle pdb=" ND1 HIS E 167 "
        pdb=" CG  HIS E 167 "
        pdb=" CD2 HIS E 167 "
      ideal   model   delta    sigma   weight residual
     106.10  109.54   -3.44 1.00e+00 1.00e+00 1.19e+01
  angle pdb=" CB  ARG B 314 "
        pdb=" CG  ARG B 314 "
        pdb=" CD  ARG B 314 "
      ideal   model   delta    sigma   weight residual
     111.30  103.41    7.89 2.30e+00 1.89e-01 1.18e+01
  ... (remaining 12355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 5080
       17.74 -    35.49: 324
       35.49 -    53.23: 55
       53.23 -    70.97: 18
       70.97 -    88.72: 5
  Dihedral angle restraints: 5482
    sinusoidal: 2174
      harmonic: 3308
  Sorted by residual:
  dihedral pdb=" CA  THR B 165 "
           pdb=" C   THR B 165 "
           pdb=" N   CYS B 166 "
           pdb=" CA  CYS B 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.61   28.39     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" CA  ALA E  92 "
           pdb=" C   ALA E  92 "
           pdb=" N   MET E  93 "
           pdb=" CA  MET E  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.03   27.97     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.32   27.68     0      5.00e+00 4.00e-02 3.07e+01
  ... (remaining 5479 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1129
       0.068 -    0.135: 257
       0.135 -    0.202: 24
       0.202 -    0.270: 3
       0.270 -    0.337: 2
  Chirality restraints: 1415
  Sorted by residual:
  chirality pdb=" C13 CLR R 601 "
            pdb=" C12 CLR R 601 "
            pdb=" C14 CLR R 601 "
            pdb=" C17 CLR R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.59   -0.34 2.00e-01 2.50e+01 2.84e+00
  chirality pdb=" C13 CLR R 602 "
            pdb=" C12 CLR R 602 "
            pdb=" C14 CLR R 602 "
            pdb=" C17 CLR R 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.62   -0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" CA  PHE B 292 "
            pdb=" N   PHE B 292 "
            pdb=" C   PHE B 292 "
            pdb=" CB  PHE B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 1412 not shown)

  Planarity restraints: 1540
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E  59 "   -0.081 2.00e-02 2.50e+03   4.15e-02 3.44e+01
        pdb=" CG  TYR E  59 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR E  59 "    0.027 2.00e-02 2.50e+03
        pdb=" CD2 TYR E  59 "    0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR E  59 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR E  59 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR E  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR E  59 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 101 "    0.059 2.00e-02 2.50e+03   3.09e-02 1.91e+01
        pdb=" CG  TYR E 101 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 101 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 101 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 101 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 101 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 101 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR E 101 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E 191 "   -0.090 9.50e-02 1.11e+02   5.24e-02 1.50e+01
        pdb=" NE  ARG E 191 "    0.027 2.00e-02 2.50e+03
        pdb=" CZ  ARG E 191 "   -0.064 2.00e-02 2.50e+03
        pdb=" NH1 ARG E 191 "    0.023 2.00e-02 2.50e+03
        pdb=" NH2 ARG E 191 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1537 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 970
        2.74 -     3.28: 9488
        3.28 -     3.82: 14879
        3.82 -     4.36: 18335
        4.36 -     4.90: 31266
  Nonbonded interactions: 74938
  Sorted by model distance:
  nonbonded pdb=" CE1 PHE B 253 "
            pdb=" CG  GLU B 260 "
     model   vdw
     2.197 3.740
  nonbonded pdb=" CD2 TYR E  50 "
            pdb=" OH  TYR E 235 "
     model   vdw
     2.236 3.340
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OH  TYR A 230 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   GLY R 165 "
            pdb=" OG  SER R 166 "
     model   vdw
     2.289 3.040
  ... (remaining 74933 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.910
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  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:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
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      :  0.008   0.060   9115  Z= 0.361
  Angle     :  0.902   7.888  12362  Z= 0.523
  Chirality :  0.057   0.337   1415
  Planarity :  0.007   0.052   1540
  Dihedral  : 12.894  88.719   3345
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  4.42 %
    Favored  : 94.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.80 (0.24), residues: 1116
  helix: -0.52 (0.25), residues: 377
  sheet:  0.32 (0.30), residues: 269
  loop : -0.91 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.005   TRP E  47 
 HIS   0.011   0.002   HIS R 143 
 PHE   0.040   0.003   PHE E 177 
 TYR   0.081   0.007   TYR E  59 
 ARG   0.065   0.009   ARG E 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14773 (  442)
  hydrogen bonds       : angle       7.08536 ( 1224)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       4.50130 (    2)
  covalent geometry    : bond        0.00808 ( 9114)
  covalent geometry    : angle       0.90013 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 200
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8393 (t70) cc_final: 0.8127 (t0)
REVERT: A  204 GLN cc_start: 0.9165 (pp30) cc_final: 0.8878 (pp30)
REVERT: B   12 GLU cc_start: 0.9425 (tp30) cc_final: 0.9176 (tp30)
REVERT: B   17 GLN cc_start: 0.9594 (tm-30) cc_final: 0.9271 (tm-30)
REVERT: B   32 GLN cc_start: 0.8902 (mt0) cc_final: 0.8662 (mt0)
REVERT: B  220 GLN cc_start: 0.9068 (mt0) cc_final: 0.8776 (mt0)
REVERT: C   58 GLU cc_start: 0.8248 (tp30) cc_final: 0.8010 (tp30)
REVERT: E   73 ASP cc_start: 0.8323 (t0) cc_final: 0.8009 (t70)
REVERT: E  120 SER cc_start: 0.8709 (t) cc_final: 0.8503 (p)
REVERT: E  230 MET cc_start: 0.9003 (tmm) cc_final: 0.8432 (ttt)
REVERT: R  167 ASP cc_start: 0.8660 (t0) cc_final: 0.8457 (t70)
REVERT: R  193 MET cc_start: 0.8832 (mtm) cc_final: 0.8614 (mtt)
REVERT: R  347 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8106 (mm-30)
REVERT: R  367 ASP cc_start: 0.8635 (m-30) cc_final: 0.8434 (m-30)
  outliers start: 7
  outliers final: 3
  residues processed: 206
  average time/residue: 0.2921
  time to fit residues: 76.9770
Evaluate side-chains
  130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 127
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  222 PHE
Chi-restraints excluded: chain R residue  215 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0670
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.2126

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
B  62 HIS
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
B 293 ASN
B 295 ASN
B 340 ASN
C  24 ASN
R 330 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.084051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.059958 restraints weight = 21623.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 3.31
r_work: 0.2769 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9115  Z= 0.147
  Angle     :  0.647   7.162  12362  Z= 0.346
  Chirality :  0.044   0.207   1415
  Planarity :  0.005   0.050   1540
  Dihedral  :  6.910  54.350   1359
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.15 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.44 (0.25), residues: 1116
  helix:  1.21 (0.26), residues: 370
  sheet:  0.30 (0.29), residues: 284
  loop : -0.37 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 339 
 HIS   0.005   0.001   HIS R 143 
 PHE   0.022   0.001   PHE A 196 
 TYR   0.029   0.002   TYR E 235 
 ARG   0.006   0.001   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04303 (  442)
  hydrogen bonds       : angle       5.33857 ( 1224)
  SS BOND              : bond        0.00418 (    1)
  SS BOND              : angle       2.09654 (    2)
  covalent geometry    : bond        0.00327 ( 9114)
  covalent geometry    : angle       0.64674 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 1.006 
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   20 ASP cc_start: 0.8736 (t70) cc_final: 0.8437 (t0)
REVERT: A  204 GLN cc_start: 0.9270 (pp30) cc_final: 0.8659 (pp30)
REVERT: A  243 MET cc_start: 0.8599 (tpp) cc_final: 0.7372 (tpp)
REVERT: B   10 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8919 (mp0)
REVERT: B  215 GLU cc_start: 0.9153 (mp0) cc_final: 0.8580 (mp0)
REVERT: C   58 GLU cc_start: 0.8720 (tp30) cc_final: 0.8382 (tp30)
REVERT: E   62 ASP cc_start: 0.9101 (m-30) cc_final: 0.8889 (p0)
REVERT: E   93 MET cc_start: 0.8760 (tpp) cc_final: 0.8556 (tpp)
REVERT: E  120 SER cc_start: 0.8638 (t) cc_final: 0.8390 (p)
REVERT: E  220 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8489 (mp0)
REVERT: E  223 ASP cc_start: 0.9202 (m-30) cc_final: 0.8791 (m-30)
REVERT: E  244 LYS cc_start: 0.9234 (tttt) cc_final: 0.8918 (tptp)
REVERT: E  246 GLU cc_start: 0.7297 (pm20) cc_final: 0.7056 (pm20)
REVERT: R  167 ASP cc_start: 0.8752 (t0) cc_final: 0.8474 (t70)
REVERT: R  347 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8308 (mm-30)
  outliers start: 23
  outliers final: 9
  residues processed: 153
  average time/residue: 0.2369
  time to fit residues: 48.8581
Evaluate side-chains
  133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   57 SER
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain R residue  110 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 77 optimal weight:    0.1980
   chunk 94 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.084904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.061032 restraints weight = 21684.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 3.33
r_work: 0.2780 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9115  Z= 0.133
  Angle     :  0.596   7.077  12362  Z= 0.316
  Chirality :  0.042   0.190   1415
  Planarity :  0.004   0.051   1540
  Dihedral  :  5.908  51.482   1356
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.10 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.70 (0.25), residues: 1116
  helix:  1.49 (0.27), residues: 370
  sheet:  0.51 (0.30), residues: 280
  loop : -0.33 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.026   0.001   PHE E  68 
 TYR   0.022   0.002   TYR E 235 
 ARG   0.004   0.000   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  442)
  hydrogen bonds       : angle       5.02769 ( 1224)
  SS BOND              : bond        0.00224 (    1)
  SS BOND              : angle       1.87550 (    2)
  covalent geometry    : bond        0.00295 ( 9114)
  covalent geometry    : angle       0.59592 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8753 (t70) cc_final: 0.8460 (t0)
REVERT: A  204 GLN cc_start: 0.9212 (pp30) cc_final: 0.8624 (pp30)
REVERT: A  243 MET cc_start: 0.8490 (tpp) cc_final: 0.7540 (tpp)
REVERT: B   12 GLU cc_start: 0.9191 (tp30) cc_final: 0.8850 (tp30)
REVERT: B   13 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8900 (mm-40)
REVERT: B  307 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8988 (t)
REVERT: C   17 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9309 (tm-30)
REVERT: C   20 LYS cc_start: 0.9422 (pptt) cc_final: 0.9146 (pptt)
REVERT: C   58 GLU cc_start: 0.8667 (tp30) cc_final: 0.8310 (tp30)
REVERT: E   62 ASP cc_start: 0.9106 (m-30) cc_final: 0.8865 (p0)
REVERT: E   73 ASP cc_start: 0.8012 (t0) cc_final: 0.7570 (t70)
REVERT: E   76 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8902 (mtpp)
REVERT: E   93 MET cc_start: 0.8789 (tpp) cc_final: 0.8575 (tpp)
REVERT: E  120 SER cc_start: 0.8703 (t) cc_final: 0.8485 (p)
REVERT: E  220 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8469 (mp0)
REVERT: E  223 ASP cc_start: 0.9224 (m-30) cc_final: 0.8453 (m-30)
REVERT: E  230 MET cc_start: 0.8950 (tmm) cc_final: 0.8687 (ttm)
REVERT: E  244 LYS cc_start: 0.9257 (tttt) cc_final: 0.8966 (tptp)
REVERT: E  246 GLU cc_start: 0.7331 (pm20) cc_final: 0.6985 (pm20)
REVERT: R  132 LYS cc_start: 0.8690 (pttm) cc_final: 0.8261 (pptt)
REVERT: R  167 ASP cc_start: 0.8650 (t0) cc_final: 0.8376 (t70)
REVERT: R  347 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8252 (mm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 150
  average time/residue: 0.2190
  time to fit residues: 45.3607
Evaluate side-chains
  138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  215 THR
Chi-restraints excluded: chain R residue  355 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 88 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 14 optimal weight:   20.0000
   chunk 99 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 108 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0470
   chunk 39 optimal weight:    3.9990
   chunk 76 optimal weight:    0.2980
   chunk 97 optimal weight:    0.0970
   overall best weight:    0.4476

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.086644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.062971 restraints weight = 21457.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 3.32
r_work: 0.2831 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9115  Z= 0.108
  Angle     :  0.566   7.499  12362  Z= 0.295
  Chirality :  0.041   0.181   1415
  Planarity :  0.004   0.055   1540
  Dihedral  :  5.315  46.785   1356
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.02 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.80 (0.25), residues: 1116
  helix:  1.49 (0.27), residues: 377
  sheet:  0.65 (0.30), residues: 278
  loop : -0.28 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.016   0.001   PHE A 196 
 TYR   0.019   0.001   TYR E 235 
 ARG   0.004   0.000   ARG B 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  442)
  hydrogen bonds       : angle       4.75765 ( 1224)
  SS BOND              : bond        0.00146 (    1)
  SS BOND              : angle       2.04689 (    2)
  covalent geometry    : bond        0.00232 ( 9114)
  covalent geometry    : angle       0.56537 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8727 (t70) cc_final: 0.8449 (t0)
REVERT: A  204 GLN cc_start: 0.9161 (pp30) cc_final: 0.8567 (pp30)
REVERT: A  306 GLN cc_start: 0.9306 (mm-40) cc_final: 0.8878 (mm-40)
REVERT: B   10 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8667 (mp0)
REVERT: B   32 GLN cc_start: 0.8911 (mt0) cc_final: 0.8607 (mt0)
REVERT: C   17 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9200 (tm-30)
REVERT: C   38 MET cc_start: 0.8485 (ptm) cc_final: 0.8226 (ptm)
REVERT: C   58 GLU cc_start: 0.8719 (tp30) cc_final: 0.8373 (tp30)
REVERT: E   62 ASP cc_start: 0.9056 (m-30) cc_final: 0.8759 (p0)
REVERT: E   73 ASP cc_start: 0.7962 (t0) cc_final: 0.7514 (t70)
REVERT: E  120 SER cc_start: 0.8696 (t) cc_final: 0.8495 (p)
REVERT: E  183 GLN cc_start: 0.8823 (mt0) cc_final: 0.8608 (pt0)
REVERT: E  223 ASP cc_start: 0.9155 (m-30) cc_final: 0.8310 (m-30)
REVERT: E  230 MET cc_start: 0.8868 (tmm) cc_final: 0.8630 (ttm)
REVERT: E  244 LYS cc_start: 0.9218 (tttt) cc_final: 0.8909 (tptp)
REVERT: E  246 GLU cc_start: 0.7415 (pm20) cc_final: 0.7119 (pm20)
REVERT: R  134 LYS cc_start: 0.8700 (ptpp) cc_final: 0.7963 (ptpp)
REVERT: R  158 LYS cc_start: 0.9393 (mttm) cc_final: 0.9182 (mttt)
REVERT: R  167 ASP cc_start: 0.8625 (t0) cc_final: 0.8352 (t70)
REVERT: R  347 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8207 (mm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 159
  average time/residue: 0.2196
  time to fit residues: 48.1590
Evaluate side-chains
  139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain R residue  215 THR
Chi-restraints excluded: chain R residue  355 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 99 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 72 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
R 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.085506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.061871 restraints weight = 21359.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 3.32
r_work: 0.2802 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9115  Z= 0.123
  Angle     :  0.577   8.713  12362  Z= 0.300
  Chirality :  0.042   0.279   1415
  Planarity :  0.004   0.053   1540
  Dihedral  :  5.209  48.374   1356
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 12.64 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.85 (0.26), residues: 1116
  helix:  1.57 (0.27), residues: 377
  sheet:  0.69 (0.31), residues: 278
  loop : -0.29 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.021   0.001   PHE E  68 
 TYR   0.026   0.001   TYR E 235 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  442)
  hydrogen bonds       : angle       4.76134 ( 1224)
  SS BOND              : bond        0.00163 (    1)
  SS BOND              : angle       1.67847 (    2)
  covalent geometry    : bond        0.00276 ( 9114)
  covalent geometry    : angle       0.57652 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8745 (t70) cc_final: 0.8450 (t0)
REVERT: A   32 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8251 (ttm-80)
REVERT: A  204 GLN cc_start: 0.9127 (pp30) cc_final: 0.8584 (pp30)
REVERT: A  261 ASP cc_start: 0.9225 (p0) cc_final: 0.9004 (p0)
REVERT: A  287 TYR cc_start: 0.8949 (m-80) cc_final: 0.8520 (m-80)
REVERT: B   10 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8590 (mp0)
REVERT: B   32 GLN cc_start: 0.8907 (mt0) cc_final: 0.8598 (mt0)
REVERT: C   17 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9325 (tm-30)
REVERT: C   38 MET cc_start: 0.8444 (ptm) cc_final: 0.8240 (ptm)
REVERT: C   58 GLU cc_start: 0.8735 (tp30) cc_final: 0.8369 (tp30)
REVERT: E   62 ASP cc_start: 0.9132 (m-30) cc_final: 0.8791 (p0)
REVERT: E   73 ASP cc_start: 0.8093 (t0) cc_final: 0.7756 (t70)
REVERT: E  223 ASP cc_start: 0.9097 (m-30) cc_final: 0.8739 (m-30)
REVERT: E  244 LYS cc_start: 0.9226 (tttt) cc_final: 0.8928 (tptp)
REVERT: E  246 GLU cc_start: 0.7313 (pm20) cc_final: 0.7061 (pm20)
REVERT: R  141 MET cc_start: 0.9095 (mmm) cc_final: 0.8690 (mmm)
REVERT: R  148 ASP cc_start: 0.8969 (m-30) cc_final: 0.8591 (t0)
REVERT: R  158 LYS cc_start: 0.9394 (mttm) cc_final: 0.9187 (mttt)
REVERT: R  167 ASP cc_start: 0.8653 (t0) cc_final: 0.8383 (t70)
REVERT: R  347 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8232 (mm-30)
  outliers start: 25
  outliers final: 14
  residues processed: 147
  average time/residue: 0.2236
  time to fit residues: 45.2835
Evaluate side-chains
  138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   10 GLU
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  215 THR
Chi-restraints excluded: chain R residue  355 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 62 optimal weight:    9.9990
   chunk 83 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
B 119 ASN
B 176 GLN
** E 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 120 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.083893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.059747 restraints weight = 21423.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 3.32
r_work: 0.2765 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9115  Z= 0.155
  Angle     :  0.584   7.336  12362  Z= 0.307
  Chirality :  0.042   0.173   1415
  Planarity :  0.004   0.055   1540
  Dihedral  :  5.260  50.247   1356
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.26 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.76 (0.26), residues: 1116
  helix:  1.47 (0.27), residues: 383
  sheet:  0.68 (0.31), residues: 278
  loop : -0.38 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 100 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.014   0.001   PHE A 196 
 TYR   0.029   0.001   TYR E 235 
 ARG   0.005   0.000   ARG E 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03625 (  442)
  hydrogen bonds       : angle       4.75338 ( 1224)
  SS BOND              : bond        0.00830 (    1)
  SS BOND              : angle       1.77716 (    2)
  covalent geometry    : bond        0.00356 ( 9114)
  covalent geometry    : angle       0.58334 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8786 (t70) cc_final: 0.8460 (t0)
REVERT: A   22 ASN cc_start: 0.9053 (m-40) cc_final: 0.8838 (t0)
REVERT: A   32 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8299 (ttm-80)
REVERT: A  204 GLN cc_start: 0.9154 (pp30) cc_final: 0.8549 (pp30)
REVERT: A  261 ASP cc_start: 0.9271 (p0) cc_final: 0.9048 (p0)
REVERT: B   32 GLN cc_start: 0.8944 (mt0) cc_final: 0.8614 (mt0)
REVERT: B  307 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (t)
REVERT: C   58 GLU cc_start: 0.8822 (tp30) cc_final: 0.8430 (tp30)
REVERT: E   62 ASP cc_start: 0.9203 (m-30) cc_final: 0.8903 (p0)
REVERT: E   73 ASP cc_start: 0.8060 (t0) cc_final: 0.7702 (t70)
REVERT: E  153 GLU cc_start: 0.8695 (pt0) cc_final: 0.8408 (pm20)
REVERT: E  223 ASP cc_start: 0.9111 (m-30) cc_final: 0.8736 (m-30)
REVERT: E  244 LYS cc_start: 0.9189 (tttt) cc_final: 0.8883 (tptp)
REVERT: R  141 MET cc_start: 0.9128 (mmm) cc_final: 0.8692 (mmm)
REVERT: R  148 ASP cc_start: 0.9085 (m-30) cc_final: 0.8654 (t0)
REVERT: R  158 LYS cc_start: 0.9373 (mttm) cc_final: 0.9168 (mttt)
REVERT: R  167 ASP cc_start: 0.8558 (t0) cc_final: 0.8303 (t70)
REVERT: R  347 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8374 (mm-30)
REVERT: R  367 ASP cc_start: 0.8847 (m-30) cc_final: 0.8627 (m-30)
  outliers start: 25
  outliers final: 18
  residues processed: 141
  average time/residue: 0.2303
  time to fit residues: 44.5446
Evaluate side-chains
  138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  176 GLN
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  215 THR
Chi-restraints excluded: chain R residue  355 LEU
Chi-restraints excluded: chain R residue  360 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    0.4980
   chunk 24 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 104 optimal weight:    8.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** E 183 GLN ** 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 = 0.3453 r_free = 0.3453 target = 0.085313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.061588 restraints weight = 21539.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.34
r_work: 0.2795 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9115  Z= 0.118
  Angle     :  0.573   7.399  12362  Z= 0.301
  Chirality :  0.041   0.153   1415
  Planarity :  0.004   0.055   1540
  Dihedral  :  5.082  48.556   1356
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.80 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.87 (0.26), residues: 1116
  helix:  1.60 (0.27), residues: 379
  sheet:  0.69 (0.31), residues: 278
  loop : -0.30 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 339 
 HIS   0.003   0.000   HIS B 225 
 PHE   0.022   0.001   PHE E  68 
 TYR   0.022   0.001   TYR E 235 
 ARG   0.003   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03459 (  442)
  hydrogen bonds       : angle       4.68234 ( 1224)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       1.63810 (    2)
  covalent geometry    : bond        0.00267 ( 9114)
  covalent geometry    : angle       0.57286 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8749 (t70) cc_final: 0.8432 (t0)
REVERT: A   32 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8217 (ttm-80)
REVERT: A  204 GLN cc_start: 0.9082 (pp30) cc_final: 0.8541 (pp30)
REVERT: B   32 GLN cc_start: 0.8944 (mt0) cc_final: 0.8616 (mt0)
REVERT: B  259 GLN cc_start: 0.8020 (tt0) cc_final: 0.7521 (mt0)
REVERT: B  307 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8915 (t)
REVERT: C   58 GLU cc_start: 0.8774 (tp30) cc_final: 0.8393 (tp30)
REVERT: E   62 ASP cc_start: 0.9154 (m-30) cc_final: 0.8802 (p0)
REVERT: E   73 ASP cc_start: 0.8104 (t0) cc_final: 0.7702 (t70)
REVERT: E  153 GLU cc_start: 0.8696 (pt0) cc_final: 0.8391 (pm20)
REVERT: E  192 MET cc_start: 0.9121 (ttp) cc_final: 0.8789 (ttp)
REVERT: E  222 GLU cc_start: 0.8536 (pm20) cc_final: 0.8303 (pm20)
REVERT: E  223 ASP cc_start: 0.9142 (m-30) cc_final: 0.8514 (m-30)
REVERT: R  127 PHE cc_start: 0.8829 (m-10) cc_final: 0.8628 (m-10)
REVERT: R  141 MET cc_start: 0.9098 (mmm) cc_final: 0.8670 (mmm)
REVERT: R  148 ASP cc_start: 0.8994 (m-30) cc_final: 0.8633 (t0)
REVERT: R  347 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8343 (mm-30)
REVERT: R  367 ASP cc_start: 0.8820 (m-30) cc_final: 0.8609 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 145
  average time/residue: 0.2350
  time to fit residues: 46.0589
Evaluate side-chains
  141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain R residue  355 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    0.0030
   chunk 28 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 104 optimal weight:    9.9990
   chunk 62 optimal weight:    8.9990
   chunk 100 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 105 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
** E 183 GLN ** 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 = 0.3466 r_free = 0.3466 target = 0.086235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.062263 restraints weight = 21786.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 3.44
r_work: 0.2817 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9115  Z= 0.114
  Angle     :  0.584   8.384  12362  Z= 0.304
  Chirality :  0.041   0.153   1415
  Planarity :  0.003   0.052   1540
  Dihedral  :  4.953  48.040   1356
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.18 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.81 (0.26), residues: 1116
  helix:  1.58 (0.27), residues: 385
  sheet:  0.63 (0.31), residues: 281
  loop : -0.37 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.003   0.000   HIS B 225 
 PHE   0.023   0.001   PHE E  68 
 TYR   0.021   0.001   TYR E 235 
 ARG   0.003   0.000   ARG E 218 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03276 (  442)
  hydrogen bonds       : angle       4.57340 ( 1224)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       1.60010 (    2)
  covalent geometry    : bond        0.00258 ( 9114)
  covalent geometry    : angle       0.58372 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 1.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8751 (t70) cc_final: 0.8452 (t0)
REVERT: A   32 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8200 (ttm-80)
REVERT: A   53 MET cc_start: 0.9160 (mpp) cc_final: 0.8935 (mpp)
REVERT: A  256 ASN cc_start: 0.8380 (t0) cc_final: 0.8056 (t0)
REVERT: B   32 GLN cc_start: 0.9023 (mt0) cc_final: 0.8767 (mt0)
REVERT: B  259 GLN cc_start: 0.8048 (tt0) cc_final: 0.7561 (mt0)
REVERT: C   58 GLU cc_start: 0.8822 (tp30) cc_final: 0.8447 (tp30)
REVERT: E   62 ASP cc_start: 0.9137 (m-30) cc_final: 0.8828 (p0)
REVERT: E   73 ASP cc_start: 0.8188 (t0) cc_final: 0.7753 (t70)
REVERT: E  153 GLU cc_start: 0.8728 (pt0) cc_final: 0.8313 (pm20)
REVERT: E  223 ASP cc_start: 0.9062 (m-30) cc_final: 0.8720 (m-30)
REVERT: R  131 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7358 (ptp)
REVERT: R  141 MET cc_start: 0.9110 (mmm) cc_final: 0.8715 (mmm)
REVERT: R  148 ASP cc_start: 0.9027 (m-30) cc_final: 0.8628 (t0)
REVERT: R  167 ASP cc_start: 0.8339 (t0) cc_final: 0.7923 (t70)
REVERT: R  258 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: R  347 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8295 (mm-30)
  outliers start: 23
  outliers final: 12
  residues processed: 149
  average time/residue: 0.2239
  time to fit residues: 45.6861
Evaluate side-chains
  134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain R residue  131 MET
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  215 THR
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  355 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 4 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 76 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** E 183 GLN ** 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 = 0.3423 r_free = 0.3423 target = 0.083442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.059219 restraints weight = 21722.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2921 rms_B_bonded: 3.35
r_work: 0.2756 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9115  Z= 0.178
  Angle     :  0.637   8.434  12362  Z= 0.331
  Chirality :  0.042   0.177   1415
  Planarity :  0.004   0.055   1540
  Dihedral  :  5.190  50.456   1356
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.21 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.78 (0.26), residues: 1116
  helix:  1.58 (0.27), residues: 385
  sheet:  0.59 (0.31), residues: 281
  loop : -0.40 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 100 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.020   0.001   PHE E  68 
 TYR   0.025   0.001   TYR E 235 
 ARG   0.003   0.000   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03663 (  442)
  hydrogen bonds       : angle       4.66321 ( 1224)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       1.58645 (    2)
  covalent geometry    : bond        0.00412 ( 9114)
  covalent geometry    : angle       0.63626 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8831 (t70) cc_final: 0.8473 (t0)
REVERT: A   22 ASN cc_start: 0.9103 (m-40) cc_final: 0.8891 (t0)
REVERT: A   32 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8274 (ttm-80)
REVERT: A  256 ASN cc_start: 0.8461 (t0) cc_final: 0.8163 (t0)
REVERT: B   32 GLN cc_start: 0.9078 (mt0) cc_final: 0.8729 (mt0)
REVERT: B  259 GLN cc_start: 0.8106 (tt0) cc_final: 0.7650 (mt0)
REVERT: C   58 GLU cc_start: 0.8847 (tp30) cc_final: 0.8454 (tp30)
REVERT: E   62 ASP cc_start: 0.9184 (m-30) cc_final: 0.8869 (p0)
REVERT: E   73 ASP cc_start: 0.8329 (t0) cc_final: 0.7950 (t70)
REVERT: E   93 MET cc_start: 0.8896 (tpp) cc_final: 0.8644 (tpp)
REVERT: E  223 ASP cc_start: 0.9016 (m-30) cc_final: 0.8766 (m-30)
REVERT: E  244 LYS cc_start: 0.9202 (tttm) cc_final: 0.8624 (tptp)
REVERT: E  246 GLU cc_start: 0.7899 (pm20) cc_final: 0.7569 (pm20)
REVERT: R  141 MET cc_start: 0.9094 (mmm) cc_final: 0.8688 (mmm)
REVERT: R  148 ASP cc_start: 0.8922 (m-30) cc_final: 0.8555 (t0)
REVERT: R  167 ASP cc_start: 0.8396 (t0) cc_final: 0.7999 (t70)
REVERT: R  258 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8353 (mp)
REVERT: R  260 GLU cc_start: 0.8455 (pm20) cc_final: 0.8206 (pm20)
REVERT: R  347 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8339 (mm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 134
  average time/residue: 0.2215
  time to fit residues: 40.8130
Evaluate side-chains
  135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue  189 ILE
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  131 MET
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  215 THR
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  355 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0370
   chunk 104 optimal weight:    4.9990
   overall best weight:    1.3464

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

Flipped N/Q/H residues before XYZ refinement:
** E 183 GLN ** 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 = 0.3447 r_free = 0.3447 target = 0.084702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.060735 restraints weight = 21435.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 3.32
r_work: 0.2785 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.4024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9115  Z= 0.138
  Angle     :  0.628  11.793  12362  Z= 0.322
  Chirality :  0.041   0.160   1415
  Planarity :  0.003   0.056   1540
  Dihedral  :  5.059  49.382   1356
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.80 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.75 (0.26), residues: 1116
  helix:  1.57 (0.27), residues: 385
  sheet:  0.54 (0.30), residues: 281
  loop : -0.40 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.017   0.001   PHE E  68 
 TYR   0.021   0.001   TYR E 235 
 ARG   0.003   0.000   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  442)
  hydrogen bonds       : angle       4.61288 ( 1224)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       1.59902 (    2)
  covalent geometry    : bond        0.00321 ( 9114)
  covalent geometry    : angle       0.62802 (12360)

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

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

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2232 Ramachandran restraints generated.
    1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8775 (t70) cc_final: 0.8438 (t0)
REVERT: A   53 MET cc_start: 0.9166 (mpp) cc_final: 0.8945 (mpp)
REVERT: A  256 ASN cc_start: 0.8368 (t0) cc_final: 0.8029 (t0)
REVERT: B   32 GLN cc_start: 0.9101 (mt0) cc_final: 0.8795 (mt0)
REVERT: B  259 GLN cc_start: 0.8065 (tt0) cc_final: 0.7635 (mt0)
REVERT: C   58 GLU cc_start: 0.8866 (tp30) cc_final: 0.8474 (tp30)
REVERT: E   46 GLU cc_start: 0.8729 (pt0) cc_final: 0.8337 (pt0)
REVERT: E   62 ASP cc_start: 0.9138 (m-30) cc_final: 0.8838 (p0)
REVERT: E   73 ASP cc_start: 0.8295 (t0) cc_final: 0.7888 (t70)
REVERT: E   93 MET cc_start: 0.8841 (tpp) cc_final: 0.8575 (tpp)
REVERT: E  153 GLU cc_start: 0.8774 (pt0) cc_final: 0.8311 (pm20)
REVERT: E  186 GLN cc_start: 0.9024 (pt0) cc_final: 0.8776 (pt0)
REVERT: E  223 ASP cc_start: 0.8998 (m-30) cc_final: 0.8422 (m-30)
REVERT: E  244 LYS cc_start: 0.9183 (tttm) cc_final: 0.8588 (tptp)
REVERT: E  246 GLU cc_start: 0.7878 (pm20) cc_final: 0.7532 (pm20)
REVERT: R  141 MET cc_start: 0.9112 (mmm) cc_final: 0.8682 (mmm)
REVERT: R  148 ASP cc_start: 0.9000 (m-30) cc_final: 0.8606 (t0)
REVERT: R  167 ASP cc_start: 0.8363 (t0) cc_final: 0.7979 (t70)
REVERT: R  258 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8109 (mp)
REVERT: R  260 GLU cc_start: 0.8437 (pm20) cc_final: 0.8145 (pm20)
REVERT: R  347 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8322 (mm-30)
  outliers start: 21
  outliers final: 18
  residues processed: 136
  average time/residue: 0.2796
  time to fit residues: 53.2460
Evaluate side-chains
  134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   41 CYS
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue  138 ILE
Chi-restraints excluded: chain R residue  110 THR
Chi-restraints excluded: chain R residue  131 MET
Chi-restraints excluded: chain R residue  155 LEU
Chi-restraints excluded: chain R residue  215 THR
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  355 LEU
Chi-restraints excluded: chain R residue  360 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 80 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
** E 183 GLN ** 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 = 0.3467 r_free = 0.3467 target = 0.085535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.061722 restraints weight = 21408.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 3.32
r_work: 0.2805 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.4139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9115  Z= 0.126
  Angle     :  0.631  11.191  12362  Z= 0.323
  Chirality :  0.041   0.160   1415
  Planarity :  0.003   0.053   1540
  Dihedral  :  4.984  48.327   1356
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.80 %
    Favored  : 83.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.73 (0.26), residues: 1116
  helix:  1.58 (0.27), residues: 385
  sheet:  0.53 (0.30), residues: 278
  loop : -0.44 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.003   0.000   HIS B 225 
 PHE   0.014   0.001   PHE A 196 
 TYR   0.038   0.001   TYR E 235 
 ARG   0.004   0.000   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03334 (  442)
  hydrogen bonds       : angle       4.52525 ( 1224)
  SS BOND              : bond        0.00111 (    1)
  SS BOND              : angle       1.55343 (    2)
  covalent geometry    : bond        0.00292 ( 9114)
  covalent geometry    : angle       0.63071 (12360)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5212.64 seconds
wall clock time: 92 minutes 2.69 seconds (5522.69 seconds total)