Starting phenix.real_space_refine
on Wed Sep 25 16:17:52 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/09_2024/7ew0_31343.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/09_2024/7ew0_31343.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/09_2024/7ew0_31343.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/09_2024/7ew0_31343.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/09_2024/7ew0_31343.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/09_2024/7ew0_31343.cif"
  }
  resolution = 3.42
  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=   0.002 sd=   0.076
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 1983 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      64      5.16       5
     C    5734      2.51       5
     N    1519      2.21       5
     O    1670      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 8987
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1838
          Classifications: {'peptide': 228}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 225}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 445
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "D"
      Number of atoms: 2280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2280
          Classifications: {'peptide': 284}
          Link IDs: {'PTRANS': 6, 'TRANS': 277}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'JEU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.29, per 1000 atoms: 0.59
  Number of scatterers: 8987
  At special positions: 0
  Unit cell: (96.05, 123.25, 129.2, 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      64     16.00
     O    1670      8.00
     N    1519      7.00
     C    5734      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS D 184 " - pdb=" SG  CYS D 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 282 " - pdb=" SG  CYS D 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 159 " - pdb=" SG  CYS E 229 " 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: 2.19
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 12 sheets defined
      36.9% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 30
      removed outlier: 3.542A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.568A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.876A  pdb=" N   GLU A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 281
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.997A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.757A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 351
      removed outlier: 3.725A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   CYS A 351 " --> pdb=" O   ASN A 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 26
      removed outlier: 3.900A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.700A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 23
      removed outlier: 4.368A  pdb=" N   GLN C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.890A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'D' and resid 23 through 33
      removed outlier: 3.586A  pdb=" N   ARG D  27 " --> pdb=" O   ASP D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 73
      removed outlier: 3.819A  pdb=" N   THR D  73 " --> pdb=" O   THR D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 78 through 105
      removed outlier: 3.852A  pdb=" N   TYR D  82 " --> pdb=" O   ARG D  78 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE D  83 " --> pdb=" O   PRO D  79 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ILE D  84 " --> pdb=" O   MET D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 110
      removed outlier: 3.810A  pdb=" N   THR D 109 " --> pdb=" O   GLY D 106 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   TYR D 110 " --> pdb=" O   ALA D 107 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 106 through 110'
    Processing helix  chain 'D' and resid 113 through 148
      removed outlier: 3.514A  pdb=" N   LEU D 136 " --> pdb=" O   VAL D 132 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ALA D 139 " --> pdb=" O   LEU D 135 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   LYS D 148 " --> pdb=" O   ILE D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 156 through 181
      removed outlier: 4.366A  pdb=" N   LEU D 160 " --> pdb=" O   ASN D 156 " (cutoff:3.500A)
      Proline residue:  D 178  - end of helix
    Processing helix  chain 'D' and resid 199 through 236
      removed outlier: 3.540A  pdb=" N   ILE D 203 " --> pdb=" O   HIS D 199 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   TYR D 225 " --> pdb=" O   TYR D 221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 269
      removed outlier: 3.928A  pdb=" N   SER D 263 " --> pdb=" O   ILE D 259 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE D 265 " --> pdb=" O   VAL D 261 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE D 266 " --> pdb=" O   LEU D 262 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 282
      removed outlier: 3.645A  pdb=" N   PHE D 273 " --> pdb=" O   TRP D 269 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   VAL D 280 " --> pdb=" O   LEU D 276 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   GLY D 281 " --> pdb=" O   LEU D 277 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 292
    Processing helix  chain 'D' and resid 295 through 314
      removed outlier: 4.177A  pdb=" N   LEU D 299 " --> pdb=" O   TYR D 295 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ALA D 300 " --> pdb=" O   PHE D 296 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   SER D 304 " --> pdb=" O   ALA D 300 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY D 305 " --> pdb=" O   VAL D 301 " (cutoff:3.500A)
      Proline residue:  D 308  - end of helix
    Processing helix  chain 'D' and resid 315 through 325
      removed outlier: 3.686A  pdb=" N   ARG D 319 " --> pdb=" O   ASN D 315 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190
      removed outlier: 3.589A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.190A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 5.941A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 3.754A  pdb=" N   ARG B  46 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ASN B 340 " --> pdb=" O   ARG B  46 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.186A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA B  73 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.679A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER B 122 " --> pdb=" O   CYS B 114 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.193A  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 151
      removed outlier: 6.945A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192
      removed outlier: 3.621A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.327A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234
      removed outlier: 3.774A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.819A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.551A  pdb=" N   SER E  25 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL E   5 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60
      removed outlier: 3.563A  pdb=" N   TYR E  50 " --> pdb=" O   TYR E  59 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142
      removed outlier: 3.623A  pdb=" N   VAL E 155 " --> pdb=" O   ILE E 216 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.585A  pdb=" N   VAL E 147 " --> pdb=" O   GLU E 246 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL E 226 " --> pdb=" O   GLN E 179 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE E 177 " --> pdb=" O   TYR E 228 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    385 hydrogen bonds defined for protein.
    1098 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1443
        1.28 -     1.41: 2324
        1.41 -     1.54: 5300
        1.54 -     1.68: 10
        1.68 -     1.81: 91
  Bond restraints: 9168
  Sorted by residual:
  bond pdb=" C22 JEU D 401 "
       pdb=" O27 JEU D 401 "
    ideal  model  delta    sigma   weight residual
    1.322  1.427 -0.105 2.00e-02 2.50e+03 2.77e+01
  bond pdb=" C23 JEU D 401 "
       pdb=" C25 JEU D 401 "
    ideal  model  delta    sigma   weight residual
    1.424  1.526 -0.102 2.00e-02 2.50e+03 2.58e+01
  bond pdb=" C13 JEU D 401 "
       pdb=" C14 JEU D 401 "
    ideal  model  delta    sigma   weight residual
    1.461  1.409  0.052 2.00e-02 2.50e+03 6.73e+00
  bond pdb=" C   VAL D 132 "
       pdb=" O   VAL D 132 "
    ideal  model  delta    sigma   weight residual
    1.237  1.208  0.029 1.17e-02 7.31e+03 6.02e+00
  bond pdb=" C   ARG E 191 "
       pdb=" O   ARG E 191 "
    ideal  model  delta    sigma   weight residual
    1.242  1.217  0.024 1.00e-02 1.00e+04 5.81e+00
  ... (remaining 9163 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 12262
        2.35 -     4.71: 113
        4.71 -     7.06: 26
        7.06 -     9.42: 3
        9.42 -    11.77: 2
  Bond angle restraints: 12406
  Sorted by residual:
  angle pdb=" N   PHE D 237 "
        pdb=" CA  PHE D 237 "
        pdb=" C   PHE D 237 "
      ideal   model   delta    sigma   weight residual
     111.28  120.03   -8.75 1.09e+00 8.42e-01 6.45e+01
  angle pdb=" N   ILE E 189 "
        pdb=" CA  ILE E 189 "
        pdb=" C   ILE E 189 "
      ideal   model   delta    sigma   weight residual
     106.61  118.33  -11.72 1.78e+00 3.16e-01 4.33e+01
  angle pdb=" C   ILE E 189 "
        pdb=" CA  ILE E 189 "
        pdb=" CB  ILE E 189 "
      ideal   model   delta    sigma   weight residual
     111.09  103.88    7.21 1.11e+00 8.12e-01 4.22e+01
  angle pdb=" N   ARG D 234 "
        pdb=" CA  ARG D 234 "
        pdb=" C   ARG D 234 "
      ideal   model   delta    sigma   weight residual
     111.36  117.93   -6.57 1.09e+00 8.42e-01 3.63e+01
  angle pdb=" N   SER E 193 "
        pdb=" CA  SER E 193 "
        pdb=" C   SER E 193 "
      ideal   model   delta    sigma   weight residual
     110.80  122.57  -11.77 2.13e+00 2.20e-01 3.05e+01
  ... (remaining 12401 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4905
       17.95 -    35.90: 434
       35.90 -    53.84: 94
       53.84 -    71.79: 11
       71.79 -    89.74: 8
  Dihedral angle restraints: 5452
    sinusoidal: 2138
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CB  CYS D 184 "
           pdb=" SG  CYS D 184 "
           pdb=" SG  CYS D 191 "
           pdb=" CB  CYS D 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.70   40.70     1      1.00e+01 1.00e-02 2.32e+01
  dihedral pdb=" SG  CYS D 184 "
           pdb=" CB  CYS D 191 "
           pdb=" SG  CYS D 191 "
           pdb=" CA  CYS D 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    1.17  -74.17     1      2.00e+01 2.50e-03 1.75e+01
  dihedral pdb=" CB  CYS D 282 "
           pdb=" SG  CYS D 282 "
           pdb=" SG  CYS D 287 "
           pdb=" CB  CYS D 287 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.95  -32.95     1      1.00e+01 1.00e-02 1.54e+01
  ... (remaining 5449 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1299
       0.072 -    0.144: 110
       0.144 -    0.217: 6
       0.217 -    0.289: 3
       0.289 -    0.361: 2
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" CA  PHE D 237 "
            pdb=" N   PHE D 237 "
            pdb=" C   PHE D 237 "
            pdb=" CB  PHE D 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.26e+00
  chirality pdb=" CA  TYR E 190 "
            pdb=" N   TYR E 190 "
            pdb=" C   TYR E 190 "
            pdb=" CB  TYR E 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  PHE D 133 "
            pdb=" N   PHE D 133 "
            pdb=" C   PHE D 133 "
            pdb=" CB  PHE D 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  ... (remaining 1417 not shown)

  Planarity restraints: 1550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 235 "   -0.012 2.00e-02 2.50e+03   2.50e-02 6.27e+00
        pdb=" C   LEU D 235 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LEU D 235 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   THR D 236 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 131 "    0.011 2.00e-02 2.50e+03   2.14e-02 4.59e+00
        pdb=" C   SER D 131 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   SER D 131 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL D 132 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 235 "    0.035 5.00e-02 4.00e+02   5.24e-02 4.40e+00
        pdb=" N   PRO E 236 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1547 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 117
        2.65 -     3.21: 7939
        3.21 -     3.77: 13067
        3.77 -     4.34: 16927
        4.34 -     4.90: 28840
  Nonbonded interactions: 66890
  Sorted by model distance:
  nonbonded pdb=" O   SER D 232 "
            pdb=" CG2 THR D 236 "
     model   vdw
     2.087 3.460
  nonbonded pdb=" OG  SER E  17 "
            pdb=" O   MET E  83 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OH  TYR B 264 "
            pdb=" O   ALA B 299 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" N   ASN E 194 "
            pdb=" OD1 ASN E 194 "
     model   vdw
     2.288 3.120
  ... (remaining 66885 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:             1.140
  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:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.140
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.105   9168  Z= 0.216
  Angle     :  0.632  11.771  12406  Z= 0.379
  Chirality :  0.044   0.361   1420
  Planarity :  0.003   0.052   1550
  Dihedral  : 14.139  89.739   3305
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  6.10 %
    Favored  : 93.18 %
  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: -1.47 (0.22), residues: 1124
  helix:  0.24 (0.25), residues: 366
  sheet: -0.73 (0.31), residues: 271
  loop : -2.04 (0.23), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 176 
 HIS   0.004   0.000   HIS E  35 
 PHE   0.010   0.001   PHE D 273 
 TYR   0.015   0.001   TYR A 230 
 ARG   0.003   0.000   ARG B   8 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 165
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
REVERT: A  306 GLN cc_start: 0.7511 (mm110) cc_final: 0.6969 (tp40)
REVERT: D   58 PHE cc_start: 0.7165 (t80) cc_final: 0.6132 (t80)
REVERT: D  141 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7189 (tm-30)
REVERT: D  183 ASN cc_start: 0.7838 (t0) cc_final: 0.7586 (t0)
REVERT: E   47 TRP cc_start: 0.7802 (t60) cc_final: 0.7602 (t60)
  outliers start: 7
  outliers final: 3
  residues processed: 170
  average time/residue: 0.2209
  time to fit residues: 51.1271
Evaluate side-chains
  127 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain E residue  193 SER
Chi-restraints excluded: chain E residue  194 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.0770
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    8.9990
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 142 HIS
D  63 ASN
D 303 ASN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9168  Z= 0.158
  Angle     :  0.537  10.621  12406  Z= 0.276
  Chirality :  0.040   0.155   1420
  Planarity :  0.003   0.049   1550
  Dihedral  :  3.944  47.462   1258
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.14 %
    Favored  : 84.33 %
  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: -0.39 (0.24), residues: 1124
  helix:  1.46 (0.27), residues: 373
  sheet: -0.30 (0.32), residues: 268
  loop : -1.63 (0.24), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  47 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.019   0.001   PHE D  58 
 TYR   0.016   0.001   TYR E 235 
 ARG   0.004   0.000   ARG D 231 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: C   42 GLU cc_start: 0.7890 (tp30) cc_final: 0.7541 (mm-30)
REVERT: D   77 HIS cc_start: 0.8026 (m90) cc_final: 0.7788 (m90)
REVERT: D  183 ASN cc_start: 0.7811 (t0) cc_final: 0.7424 (t0)
REVERT: E   34 MET cc_start: 0.7446 (mmm) cc_final: 0.7175 (mmm)
REVERT: E   47 TRP cc_start: 0.7429 (t60) cc_final: 0.7144 (t60)
REVERT: E   76 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7572 (mtmm)
REVERT: E   93 MET cc_start: 0.7418 (mpp) cc_final: 0.6999 (mmt)
  outliers start: 15
  outliers final: 9
  residues processed: 133
  average time/residue: 0.2085
  time to fit residues: 38.6099
Evaluate side-chains
  121 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain D residue   68 LEU
Chi-restraints excluded: chain D residue   80 MET
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 101 optimal weight:    8.9990
   chunk 110 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 294 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  13 GLN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 232 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   9168  Z= 0.377
  Angle     :  0.659   8.396  12406  Z= 0.346
  Chirality :  0.045   0.228   1420
  Planarity :  0.004   0.054   1550
  Dihedral  :  4.582  49.086   1255
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.17 %
    Favored  : 80.26 %
  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: -0.49 (0.24), residues: 1124
  helix:  1.46 (0.27), residues: 375
  sheet: -0.51 (0.31), residues: 253
  loop : -1.66 (0.25), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  47 
 HIS   0.005   0.002   HIS A 188 
 PHE   0.024   0.002   PHE B 241 
 TYR   0.018   0.002   TYR E 235 
 ARG   0.004   0.001   ARG B 256 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7866 (m-30)
REVERT: B  197 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7579 (tpp80)
REVERT: D  141 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: D  183 ASN cc_start: 0.7937 (t0) cc_final: 0.7570 (t0)
REVERT: D  299 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6691 (pp)
REVERT: E   34 MET cc_start: 0.7442 (mmm) cc_final: 0.7209 (mmm)
REVERT: E   76 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7791 (mtmm)
REVERT: E   93 MET cc_start: 0.7528 (mpp) cc_final: 0.7152 (mmt)
REVERT: E  177 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.6113 (p90)
  outliers start: 35
  outliers final: 18
  residues processed: 144
  average time/residue: 0.2094
  time to fit residues: 41.7350
Evaluate side-chains
  122 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   80 MET
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  177 PHE
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 11 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 102 optimal weight:    0.6980
   chunk 108 optimal weight:    8.9990
   chunk 53 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9168  Z= 0.164
  Angle     :  0.528  11.269  12406  Z= 0.272
  Chirality :  0.040   0.169   1420
  Planarity :  0.003   0.052   1550
  Dihedral  :  4.150  46.982   1255
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.92 %
    Favored  : 78.03 %
  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: -0.21 (0.25), residues: 1124
  helix:  1.81 (0.27), residues: 378
  sheet: -0.38 (0.32), residues: 254
  loop : -1.61 (0.25), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP E  47 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.022   0.001   TYR E 235 
 ARG   0.003   0.000   ARG D 234 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 120
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
REVERT: C   46 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8179 (tppp)
REVERT: D   67 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6334 (mm)
REVERT: D  141 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: D  183 ASN cc_start: 0.7829 (t0) cc_final: 0.7424 (t0)
REVERT: D  299 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6657 (pp)
REVERT: E   34 MET cc_start: 0.7423 (mmm) cc_final: 0.7170 (mmm)
REVERT: E   47 TRP cc_start: 0.7479 (t60) cc_final: 0.7167 (t60)
REVERT: E   76 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7730 (mtmm)
REVERT: E   93 MET cc_start: 0.7286 (mpp) cc_final: 0.6918 (mmt)
  outliers start: 30
  outliers final: 18
  residues processed: 143
  average time/residue: 0.2082
  time to fit residues: 41.4224
Evaluate side-chains
  129 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue   80 MET
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  177 PHE
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9168  Z= 0.239
  Angle     :  0.563   9.733  12406  Z= 0.291
  Chirality :  0.042   0.188   1420
  Planarity :  0.004   0.062   1550
  Dihedral  :  4.232  46.304   1255
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 19.53 %
    Favored  : 76.70 %
  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: -0.23 (0.25), residues: 1124
  helix:  1.84 (0.27), residues: 378
  sheet: -0.48 (0.32), residues: 249
  loop : -1.59 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.017   0.002   PHE B 241 
 TYR   0.016   0.001   TYR E 235 
 ARG   0.004   0.000   ARG A  24 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 117
  time to evaluate  : 1.086 
Fit side-chains
REVERT: B  214 ARG cc_start: 0.8217 (mpt180) cc_final: 0.7979 (mpt180)
REVERT: D   67 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6176 (mm)
REVERT: D  141 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7348 (tm-30)
REVERT: D  183 ASN cc_start: 0.7811 (t0) cc_final: 0.7384 (t0)
REVERT: D  299 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6793 (pp)
REVERT: E   34 MET cc_start: 0.7562 (mmm) cc_final: 0.7173 (mmm)
REVERT: E   47 TRP cc_start: 0.7550 (t60) cc_final: 0.7299 (t60)
REVERT: E   76 LYS cc_start: 0.8114 (mtmm) cc_final: 0.7730 (mtmm)
REVERT: E   93 MET cc_start: 0.7343 (mpp) cc_final: 0.6995 (mmt)
  outliers start: 37
  outliers final: 22
  residues processed: 145
  average time/residue: 0.2006
  time to fit residues: 40.8106
Evaluate side-chains
  134 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  177 PHE
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 108 optimal weight:    7.9990
   chunk 89 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 56 optimal weight:    7.9990
   chunk 104 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9168  Z= 0.298
  Angle     :  0.603  10.418  12406  Z= 0.312
  Chirality :  0.043   0.175   1420
  Planarity :  0.004   0.063   1550
  Dihedral  :  4.227  39.775   1253
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 19.74 %
    Favored  : 76.09 %
  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: -0.30 (0.25), residues: 1124
  helix:  1.82 (0.27), residues: 376
  sheet: -0.62 (0.31), residues: 253
  loop : -1.59 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  47 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.018   0.002   PHE A 267 
 TYR   0.013   0.001   TYR E 235 
 ARG   0.006   0.000   ARG B 256 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7918 (m-30)
REVERT: A   25 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: B  197 ARG cc_start: 0.7921 (tpp80) cc_final: 0.7711 (tpp80)
REVERT: B  219 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7509 (mtt-85)
REVERT: D   67 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6107 (mm)
REVERT: D  141 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7447 (tm-30)
REVERT: D  183 ASN cc_start: 0.7712 (t0) cc_final: 0.7235 (t0)
REVERT: D  299 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6688 (pp)
REVERT: E   34 MET cc_start: 0.7539 (mmm) cc_final: 0.7140 (mmm)
REVERT: E   47 TRP cc_start: 0.7533 (t60) cc_final: 0.7249 (t60)
REVERT: E   93 MET cc_start: 0.7394 (mpp) cc_final: 0.7055 (mmt)
  outliers start: 41
  outliers final: 34
  residues processed: 146
  average time/residue: 0.2063
  time to fit residues: 41.6723
Evaluate side-chains
  142 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 105
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  271 CYS
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   57 CYS
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  134 SER
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  139 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  177 PHE
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 79 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0010
   chunk 107 optimal weight:    8.9990
   chunk 67 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.7592

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9168  Z= 0.262
  Angle     :  0.580  10.861  12406  Z= 0.300
  Chirality :  0.042   0.170   1420
  Planarity :  0.004   0.061   1550
  Dihedral  :  4.175  40.826   1253
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.45 %
    Favored  : 75.48 %
  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: -0.37 (0.25), residues: 1124
  helix:  1.81 (0.27), residues: 377
  sheet: -0.78 (0.32), residues: 254
  loop : -1.61 (0.25), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E  47 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.016   0.002   PHE B 241 
 TYR   0.014   0.001   TYR E 235 
 ARG   0.009   0.000   ARG D 324 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 112
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7930 (m-30)
REVERT: B  197 ARG cc_start: 0.7931 (tpp80) cc_final: 0.7419 (tpp80)
REVERT: B  219 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7506 (mtt-85)
REVERT: D   67 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6129 (mm)
REVERT: D  141 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7388 (tm-30)
REVERT: D  183 ASN cc_start: 0.7592 (t0) cc_final: 0.7122 (t0)
REVERT: D  299 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6718 (pp)
REVERT: D  324 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7752 (ttp80)
REVERT: E   34 MET cc_start: 0.7549 (mmm) cc_final: 0.7171 (mmm)
REVERT: E   47 TRP cc_start: 0.7512 (t60) cc_final: 0.7234 (t60)
REVERT: E   93 MET cc_start: 0.7340 (mpp) cc_final: 0.7000 (mmt)
  outliers start: 40
  outliers final: 34
  residues processed: 144
  average time/residue: 0.2171
  time to fit residues: 42.7398
Evaluate side-chains
  144 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 107
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue   52 GLN
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  269 ASN
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   57 CYS
Chi-restraints excluded: chain D residue   67 LEU
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  167 CYS
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  228 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  139 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  177 PHE
Chi-restraints excluded: chain E residue  238 THR
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0970
   chunk 21 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0770
   chunk 10 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 103 optimal weight:    8.9990
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9168  Z= 0.134
  Angle     :  0.525  10.712  12406  Z= 0.264
  Chirality :  0.040   0.143   1420
  Planarity :  0.003   0.062   1550
  Dihedral  :  3.775  34.672   1253
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.77 %
    Favored  : 75.08 %
  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: -0.13 (0.25), residues: 1124
  helix:  2.09 (0.27), residues: 377
  sheet: -0.58 (0.32), residues: 250
  loop : -1.58 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 117 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.010   0.001   PHE D 273 
 TYR   0.012   0.001   TYR E 235 
 ARG   0.009   0.000   ARG B 256 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7917 (m-30)
REVERT: B  197 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7688 (tpp80)
REVERT: D  183 ASN cc_start: 0.7549 (t0) cc_final: 0.7080 (t0)
REVERT: D  299 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6774 (pp)
REVERT: E   34 MET cc_start: 0.7421 (mmm) cc_final: 0.7078 (mmm)
REVERT: E   47 TRP cc_start: 0.7266 (t60) cc_final: 0.6982 (t60)
REVERT: E   93 MET cc_start: 0.7203 (mpp) cc_final: 0.6826 (mmt)
REVERT: E  230 MET cc_start: 0.7677 (tpp) cc_final: 0.7225 (tpp)
  outliers start: 31
  outliers final: 28
  residues processed: 139
  average time/residue: 0.2098
  time to fit residues: 40.3514
Evaluate side-chains
  143 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   57 CYS
Chi-restraints excluded: chain D residue   80 MET
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  167 CYS
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   53 SER
Chi-restraints excluded: chain E residue  139 VAL
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  177 PHE
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.0670
   chunk 100 optimal weight:    1.9990
   chunk 103 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 78 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.7924

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9168  Z= 0.164
  Angle     :  0.540  10.641  12406  Z= 0.271
  Chirality :  0.040   0.141   1420
  Planarity :  0.004   0.066   1550
  Dihedral  :  3.726  30.149   1253
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.77 %
    Favored  : 74.87 %
  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: -0.05 (0.25), residues: 1124
  helix:  2.08 (0.27), residues: 379
  sheet: -0.48 (0.33), residues: 250
  loop : -1.51 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.002   0.001   HIS A 188 
 PHE   0.010   0.001   PHE B 241 
 TYR   0.012   0.001   TYR E 235 
 ARG   0.007   0.000   ARG B 256 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7948 (m-30)
REVERT: B  197 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7696 (tpp80)
REVERT: B  219 ARG cc_start: 0.7953 (mtp85) cc_final: 0.7578 (mtt-85)
REVERT: D  183 ASN cc_start: 0.7488 (t0) cc_final: 0.7017 (t0)
REVERT: D  299 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6769 (pp)
REVERT: D  324 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7701 (ttp80)
REVERT: E   34 MET cc_start: 0.7464 (mmm) cc_final: 0.7252 (mmm)
REVERT: E   47 TRP cc_start: 0.7449 (t60) cc_final: 0.7117 (t60)
REVERT: E   93 MET cc_start: 0.7269 (mpp) cc_final: 0.6912 (mmt)
  outliers start: 33
  outliers final: 28
  residues processed: 137
  average time/residue: 0.2282
  time to fit residues: 42.2534
Evaluate side-chains
  141 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   57 CYS
Chi-restraints excluded: chain D residue   80 MET
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  167 CYS
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   53 SER
Chi-restraints excluded: chain E residue  177 PHE
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 111 optimal weight:    0.9990
   chunk 102 optimal weight:    6.9990
   chunk 88 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9168  Z= 0.180
  Angle     :  0.542  10.454  12406  Z= 0.274
  Chirality :  0.040   0.141   1420
  Planarity :  0.004   0.065   1550
  Dihedral  :  3.736  26.860   1253
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 22.69 %
    Favored  : 74.26 %
  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: -0.01 (0.25), residues: 1124
  helix:  2.12 (0.27), residues: 378
  sheet: -0.45 (0.33), residues: 249
  loop : -1.50 (0.25), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E  47 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.012   0.001   PHE B 241 
 TYR   0.013   0.001   TYR E 235 
 ARG   0.009   0.000   ARG B 256 

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

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

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2248 Ramachandran restraints generated.
    1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7957 (m-30)
REVERT: A  247 MET cc_start: 0.8670 (mtt) cc_final: 0.8457 (mtt)
REVERT: A  302 TYR cc_start: 0.7665 (t80) cc_final: 0.7429 (t80)
REVERT: B  197 ARG cc_start: 0.7934 (tpp80) cc_final: 0.7708 (tpp80)
REVERT: B  219 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7569 (mtt-85)
REVERT: C   38 MET cc_start: 0.8045 (mmm) cc_final: 0.7813 (tpp)
REVERT: D  141 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: D  183 ASN cc_start: 0.7450 (t0) cc_final: 0.6958 (t0)
REVERT: D  299 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6829 (pp)
REVERT: D  324 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7724 (ttp80)
REVERT: E   34 MET cc_start: 0.7474 (mmm) cc_final: 0.7259 (mmm)
REVERT: E   47 TRP cc_start: 0.7493 (t60) cc_final: 0.7150 (t60)
REVERT: E   93 MET cc_start: 0.7263 (mpp) cc_final: 0.6930 (mmt)
REVERT: E  230 MET cc_start: 0.7653 (tpp) cc_final: 0.7144 (tpp)
  outliers start: 30
  outliers final: 27
  residues processed: 130
  average time/residue: 0.2177
  time to fit residues: 38.9051
Evaluate side-chains
  135 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 ASP
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain D residue   26 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   57 CYS
Chi-restraints excluded: chain D residue   80 MET
Chi-restraints excluded: chain D residue  102 LEU
Chi-restraints excluded: chain D residue  167 CYS
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  209 VAL
Chi-restraints excluded: chain D residue  299 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   22 CYS
Chi-restraints excluded: chain E residue   53 SER
Chi-restraints excluded: chain E residue  177 PHE
Chi-restraints excluded: chain E residue  243 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0980
   chunk 37 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.2980
   chunk 78 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 294 ASN
** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.181571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.135885 restraints weight = 11139.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 3.11
r_work: 0.3472 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9168  Z= 0.171
  Angle     :  0.539  10.554  12406  Z= 0.272
  Chirality :  0.040   0.132   1420
  Planarity :  0.004   0.066   1550
  Dihedral  :  3.702  23.939   1253
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 22.48 %
    Favored  : 74.16 %
  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:  0.04 (0.25), residues: 1124
  helix:  2.12 (0.27), residues: 381
  sheet: -0.38 (0.33), residues: 249
  loop : -1.49 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 211 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.012   0.001   PHE E 239 
 TYR   0.011   0.001   TYR E 235 
 ARG   0.009   0.000   ARG B 256 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2041.08 seconds
wall clock time: 37 minutes 6.01 seconds (2226.01 seconds total)